See discussions, stats, and author profiles for this publication at: https://www.researchgate.

net/publication/306315788

Research progress of plant population genomics based on high-throughput

sequencing

Article  in  Hereditas (Beijing) · August 2016

DOI: 10.16288/j.yczz.16-061

CITATIONS READS

0 100

1 author:

Wang Yunsheng

23 PUBLICATIONS   226 CITATIONS   

SEE PROFILE

Some of the authors of this publication are also working on these related projects:

population genetics resaerch View project

plant research View project

All content following this page was uploaded by Wang Yunsheng on 16 November 2021.

The user has requested enhancement of the downloaded file.

The Plant Journal (2021) doi: 10.1111/tpj.15209

Loquat (Eriobotrya japonica (Thunb.) Lindl) population

genomics suggests a two-staged domestication and
identifies genes showing convergence/parallel selective
sweeps with apple or peach
Yunsheng Wang1,*,† and Andrew H. Paterson2,3,4,†
1
College of Health and Life Science, Kaili University, Kaili City, Guizhou Province 556011, China,
2
Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30605, USA,
3
Southwest University, Chongqing, China, and
4
North China University of Science and Technology, Tangshan City, Hebei Province 063210, China

Received 18 October 2020; revised 26 January 2021; accepted 13 February 2021.

*For correspondence (e-mail wys3269@126.com).
†
These authors contributed equally.

SUMMARY
Crop domestication and evolution represent key fields of plant and genetics research. Here, we re-se-
quenced and analyzed whole genome data from 51 wild accessions and 53 representative cultivars of Eri-
obotrya japonica, an important semi-subtropical fruit crop. Population genomics analysis suggested that
modern cultivated E. japonica experienced a two-staged domestication fitting the “marginality model,”
being initially domesticated in west-northern Hubei province from a mono-phylogenetic wild progenitor,
then refined mainly in Jiangsu, Zhejiang and Fujian provinces of China. Cultivated E. japonica has experi-
enced little reduction in genome-wide nucleotide polymorphism compared with wild forms. Genes respon-
sible for sugar biosynthesis were enriched in regions harboring putative selective sweeps. An approach
based on co-clustering into gene families and evaluating chromosome colinearity of orthologous and paral-
ogous genes was used to identify convergent/parallel selective sweeps among different crops. Specifically,
more than one hundred of orthologs and paralogs undergoing selective sweeps were identified between
loquat, apple and peach, among which 14 encoded “UDP glycosyltransferase 1.” In sum, the study not only
provided valuable information for breeding of E. japonica, but also enriched knowledge of crop domestica-
tion.

Keywords: domestication genetics, high-throughput sequencing, loquat, population genomics, selective

sweep.

INTRODUCTION
Plant domestication represents a key innovation in the his-
tory of human civilization (Gepts, 2004; Olsen and Wendel,
2013). An estimated 2500 plant species belonging to 160
families have undergone domestication and are cultivated
to provide for human needs (Dirzo and Raven, 2003).
Those domesticated as fruit crops are dominant in number
(Meyer et al., 2012). Since Darwin realized the importance
of domestication for species evolution, many botanists and
geneticists have sought clues to plant domestication in
crops and their wild progenitors, and tried to clarify basic
principles including the influence on genetic diversity, its
geographic distribution, and its impact on genomic regions
and individual genes that differentiate crops from their
progenitors (Cornille et al., 2012; Morrell et al., 2012;
Schreiber et al., 2018). Recently, high-throughput sequenc-
ing platforms have accelerated progress in studying
domestication of crops such as rice (Huang et al., 2012),
maize (Hufford et al., 2012), soybean (Zhou et al., 2015),
bean (Schmutz et al., 2014), tomato (Lin et al., 2014),
cucumber (Qi et al., 2013), apple (Duan et al., 2017), pear
(Wu et al., 2018) and peach (Cao et al., 2014; Yu et al.,
2018). The corresponding findings have deepened insights
into the origin and evolution of various crops, and pro-
vided an important basis for exploring and summarizing
genetic mechanisms of crop domestication. For example,
how many and what kind of genes experienced conver-
gent/parallel artificial selection among different crops.

© 2021 Society for Experimental Biology and John Wiley & Sons Ltd 1
2 Yunsheng Wang and Andrew H. Paterson

Clarification of the problem is a key issue to domesticate evidence of convergent/parallel artificial selection between
new crops for the nutritional needs of the growing popula- loquat and apple or peach.
tion, with importance to the development of contemporary
and future agricultural civilization. RESULTS
Common loquat, Eriobotrya japonica (Thunb.) Lindl, like
Genome re-sequencing and SNPs calling
apple and peach, is a perennial Rosaceae fruit. While apple
and peach are mainly distributed in temperate and some Eriobotrya japonica genotypes chosen for genome re-se-
subtropical regions, blooming in spring and maturing in quencing included 51 wild accessions representing the
autumn, E. japonica is mainly planted in subtropical and species natural distribution, and 52 cultivars from China,
some tropical areas. It blooms in autumn and winter, and Japan, the USA, Spain, France and Italy (Figure S1; Data
matures the following spring and summer. Wild E. japon- S1). We obtained 5.01–29.22 Gb clean data from the 103 E.
ica is indigenous to subtropical mountain forests in Guiz- japonica accessions by using an Illumina Hiseq 4000 plat-
hou, Chongqing, part of Sichuan, Hunan, Hubei and form (Data S2), with the average of 6.72 Gb representing
Yunnan provinces (Lin et al., 2004). About 500 varieties approximately 99 coverage of the approximately 749-Mb
have been bred, but only about 50 are used for commercial E. japonica genome. By mapping to the reference genome
cultivation, planted in orchards in more than 30 countries of cultivar “Big Five-pointed Star,” we obtained about
including China, Japan, the USA, France, Spain and Italy 454.49 Mb non-redundant alignment sequences with 50%
(Janick et al., 2015). In 2010, the annual output of loquat in sample coverage, and identified more than 2.29 million
China accounted for about 90% of the world production of SNPs from the alignment sequences with locus integrity
1.2 million tons (Badenes et al., 2015). ≥0.8, and minor allele frequency ≥0.05 to use for further
Although the species name of common loquat is japon- analysis (Table 1).
ica, detailed documentation and conclusive archaeological
Domestication incurred little loss in genetic diversity, but
evidences show it to have first been domesticated in
significant genetic differentiation
China (Lin et al., 1999). Natural wild E. japonica popula-
tions are found only in China, and most cultivated vari- We identified almost the same number of SNPs (2 291 332
eties were bred in China. Hanyuan county of Sichuan vs. 2 291 376) in the sequence alignments of cultivated
province and Changyang county of Hubei province have and wild E. japonica populations, with averages of 4.86
been suggested to be the center of origin of E. japonica, SNPs per 1000 bases respectively. The nucleotide diversity
and the original domestication place (Zhang et al., 1990; (p) of cultivated E. japonica is 1.015 9 10 3, about 94.16%
Zhang and Zhang, 1982). However, each of these infer- of the 1.078 9 10 3 of wild E. japonica (Table 1) and very
ences are speculative, based on comparison of plant close to the average 94.8% difference between perennial
community, geography, climatic conditions, biological crops and their wild progenitors estimated by neutral
characteristics and distribution of wild E. japonica and markers (Miller and Gross, 2011). Such tiny bottlenecks
other wild loquat species. Wang et al (2017) conducted a resulting from domestication are also found in apple
preliminary study on the domestication genetics of com-
mon loquat by using a single nucleotide polymorphism
(SNP) dataset from nine wild accessions and 10 cultivars Table 1 Genetic diversity and neutrality test of wild and cultivated
generated from restriction-site associated DNA tag loquat populations
sequencing, but the sampling in that study is far from
Modern cultivated
sufficient, leaving the domestication genetics of loquat Parameters loquat Wild loquat
inadequately described.
Here, we re-sequenced and analyzed the genomes of 52 Total alignment length (bp) 454 491 432 454 491 432
n.segregating.sites 2291 332 2291 376
cultivars collected worldwide and 51 wild E. japonica
p 1.015 9 10 3 1.078 9 10 3
accessions representing the species natural distribution. ΘW 6.418 9 10 4 6.475 9 10 4
Together with a sequenced and assembled draft genome Tajima’s D 2.000 2.294
of a major loquat cultivar, “Big Five-pointed Star,” at the Fu & Li’s F 2.574 2.815
chromosome level (Wang, 2021), we undertook population Fu & Li’s D 2.259 2.388
R2 of half decay value (kb) 4.273 2.421
genetics analyses. The major aims are to clarify: (i) transi-
R2 of 0.1 decay value (kb) 147.858 24.267
tion of population structure from wild to cultivated popula- FST (cultivated loquat vs. 0.173
tions resulting from domestication; (ii) pathways and key wild loquat)
nodes of origin, domestication and migration; and (ii)
genomic sequences and genes affected by artificial selec- Π, nucleotide polymorphism; ΘW, genetic diversity. R2, linkage dis-
equilibrium coefficient.
tion. Beside, we also identified some genes showing

© 2021 Society for Experimental Biology and John Wiley & Sons Ltd,
The Plant Journal, (2021), doi: 10.1111/tpj.15209

(93.6% by Malus domestica/Malus sieversii in Kazakhstan;
86.3% by M. domestica/Malus sylvestris; 169.2% by M.
domestica/sieversii in Xinjiang) (Duan et al., 2017), pear
(Asian pears: 91.4%; European pears: 98.95%) (Wu et al.,
2018) and vitis (0.94 by vinifera/sylvestris) (Zhou et al.,
2018). This is in contrast to much greater differentiation
between domesticates and their wild relatives for rice
(80.0%) (Huang et al., 2012), maize (83.0%) (Hufford et al.,
2012), soybean (47.6%) (Zhou et al., 2015), peach (approxi-
mately 78.2–93.9%) (Cao et al., 2019), Prume mume (71.3%)
(Zhang et al., 2018) and watermelon (8.3% by Citrullus
lanatus/Citrullus colocynthis; 24.6% by C. lanatus/Citrullus
amarus; 70.7% by C. lanatus/Citrullus mucosospermus)
(Guo et al., 2019). However, the overall genetic diversity of
cultivated E. japonica is far lower than most other
sequenced perennial fruit crops such as Phoenix dactylif-
era (p = 9.2 9 10 3) (Hazzouri et al., 2015), Manihot escu-
lenta (p = 2.6 9 10 3) (Kawuki et al., 2009), P. mume
(p = 2.0 9 10 3) (Zhang et al., 2018), Pyrus bretschneideri
(p = 5.5 9 10 3) (Wu et al., 2018) and M. domestica
(p = 2.20 9 10 3) (Duan et al., 2017), implying very limited
scope for loquat breeding and improvement.
Despite very limited genetic divergence, cultivated and
wild E. japonica has experienced significant genetic differ-
entiation as estimated by fixation index (FST) of 0.173
(Table 1), larger than that between cultivated maize and its
wild progenitor (FST = 0.11) (Hufford et al., 2012). A simula-
tion showed the model of unidirectional gene flow from
wild to cultivated E. japonica to have the largest Bezier
approximated score (Table 2), implying no recent gene
flow from cultivated into wild E. japonica. This is consis-
tent with the fact that most E. japonica cultivars are
planted far away from the distribution range of wild popu-
lations. A similar pattern of gene flow was also observed
in peach (Yu et al., 2018), but not in apple where gene
introgression from wild to cultivated populations was
detected (Cornille et al., 2013; Feurtey et al., 2016). The
level of linkage disequilibrium (LD) in E. japonica also
showed clear differentiation, being far higher in cultivated
than wild populations (Figure S2). The 50% drop of LD
level (R2) in cultivated E. japonica is 4.273 kb but in the
Table 2 Gene flow between wild and cultivated loquat populations
Gene Bezier Nm (per
flow approximated generation)
model score (1b) from 2 to1
Mo1 260 137.842500 16.42
Mo2 259 010.163336
Mo3 264 987.872390 9.38
Mo4 276 697.982597
1, wild loquat population; 2, cultivated loquat population; Mo1, bidirectional gene flow between wild and cultivated loquat populations;
Mo2, unidirectional gene flow from wild to cultivated loquat population; Mo3, unidirectional gene flow from cultivated to wild loquat popu-
lation; Mo4, no gene flow between wild and cultivated loquat populations; Theta, genetic diversity.
© 2021 Society for Experimental Biology and John Wiley & Sons Ltd,
The Plant Journal, (2021), doi: 10.1111/tpj.15209
Population genomics of loquat 3
wild population is only 2.421 kb; with R2 dropping to 0.1 in
147.858 versus 24.267 kb, respectively (Table 1). Moreover,
the LD level of different E. japonica chromosomes varied
widely (Figure S2). These findings indicate that the gen-
ome-wide association study in loquat may offer very high
resolution but will require high marker densities, particu-
larly in wild germplasm where LD is small, and may need
to be at densities that are excessive for some chromo-
somes to cover others adequately.
A severe genetic bottleneck during the past 10 000 years
constrained diversity in both wild and cultivated loquat.
The D value of aligned data of both cultivated and wild
common loquat populations estimated by Tajima’s test,
and Fu and Li’s test were all >2 (Table 1), suggesting a
population bottleneck or balanced selection. Simulation
results regarding the demographic dynamic showed that
both cultivated and wild common loquat experienced a
sharp decrease in effective population size (Ne) in the past
10 000 years, the present Ne being about 2700 (wild) and
700 (cultivated) (Figure S3; Data S3).
Domestication originated from a single event in central-
west Hubei province, and finished in southern Jiangsu,
Zhejiang and Fujian provinces
The location or region where crop domestications began,
and whether the process involved single or multiple events
to form cultivated populations, are basic concerns in the
study of crop domestication. To answer these two ques-
tions, we performed a phylogenetic analysis and a popula-
tion structure analysis based on the SNP dataset from the
104 accessions sampled. A neighbor-joining phylogenetic
tree clustered all cultivated E. japonica samples together at
one end and all wild samples at the other end (Figure 1).
Population structure analysis suggested admixture, with
six genetic subpopulations (k = 6) representing the best fit
to the SNP data. The whole loquat population roughly
clustered into two wild and four cultivated subpopulations,
except that one cultivated sample (C_BQZ) clustering into
the wild subpopulation also had a high probability to clus-
ter into a cultivated subgroup. Setting k = 2, the 104 acces-
sions clustered into a cultivated subpopulation and a wild
Nm (per
generation)
from 1 to 2 Theta_1 Theta_2
17.04 0.09948 0.09961
17.27 0.09956 0.09957
0.09945 0.09964
0.09953 0.09911
4 Yunsheng Wang and Andrew H. Paterson
Figure 1. Phylogenetic tree of 104 accessions loquat samples.
subpopulation, except that two wild samples (W_HB_BK
and W_SX_PL) clustered into the cultivated subpopulation,
but both were the closest to other samples in the wild sub-
population (Figure S4).
In partial summary, we hypothesize that cultivated E.
japonica originated from a single domestication event from
a mono-phylogenetic wild progenitor, like other crops such
as rice (Huang et al., 2012), soybean (Zhou et al., 2015), maize
(Matsuoka et al., 2002), apple (Duan et al., 2017) and peach
(Cao et al., 2014; Yu et al., 2018). In the phylogenetic tree, the
wild samples marked as W_HB_BK, W_SX_PL, W_HB_YA,
W_HB_YD, W_HB_ZX and W_HB_WF showed a tree topology
consistent with the progenitor of domesticated genotypes
due to their closest genetic distance to cultivated genotypes,
and these were all collected from the northeast edge of the
range of wild E. japonica populations. Five of these were
from central-northwest Hubei province, with W_SX_PL
being from Pingli County, Shaanxi province, near Hubei pro-
vince. We speculate that this region is the birthplace of
loquat domestication (Figure 1; Figure S1, Data S1), consis-
tent with archaeological findings that the oldest known
remains of loquat seeds were found in Yilan County in this
region (Wang et al., 2017). Another fact is that most modern
loquat cultivars were bred in Jiangsu, Zhejiang and Fujian
provinces, and few were bred from other places, including
Hubei province. We deduced that the original domesticated
E. japonica diffused rapidly to other suitable cultivation
areas of China, but little breeding and selection activities
were performed and no or few varieties with excellent edible
quality were bred in regions other than Jiangsu, Zhejiang
and Fujian province, These three provinces, particularly the
© 2021 Society for Experimental Biology and John Wiley & Sons Ltd,
southern part of Jiangsu and northern part of Zhejiang, have
been an economic center in China with relatively developed
agricultural production since the Han dynasty of 2000 years
ago. The ancient domesticated loquats should have experi-
enced high selection intensity here, and many high-quality
loquat varieties were bred in this region. Therefore, Jiangsu,
Zhejiang and Fujian provinces may be regarded as a sec-
ondary domestication center (Figure S1). The outer edge of
the phylogenetic tree where wild loquat samples clustered
was almost from Guizhou province (Figure 1; Figure S1,
Data S1), implying that the existing natural loquat popula-
tion may have been born in or took refuge in Guizhou pro-
vince during the last glacial period, close to Yunnan
province, which appears to be the center of diversity of the
Eriobotrya genus (Lin et al., 2004).
Selection effect in the process of domestication
Plant domestication is an evolutionary process influenced
by human activities (Harlan, 1992). Over time, a domesti-
cated population would diverge from its wild progenitor
population and differ in morphological, physiological and
genetic characters (Pickersgill, 2007). The changed mor-
phological and physiological characters are often called
the “domestication syndrome,” and depend on corre-
sponding genetic characters called “domestication genes.”
Artificial selection may not only affect “domestication
genes,” it also reduces or eliminates nucleotide variation
in neighboring genomic sequence, causing a “selective
sweep” due to the “hitchhiking effect” (Rubin et al., 2010).
Wild-domesticated population pairs provide excellent
research systems in which to study what Darwin referred to
The Plant Journal, (2021), doi: 10.1111/tpj.15209
 Population genomics of loquat 5

as the “obscure problem” of natural selection (Purugganan cultivated loquat, putatively from balancing the selection,
and Fuller, 2009). Identification of the molecular footprints of which hold 2014 and 450 predicted protein-coding genes
selection is a central task in the study of crop domestication (Table 3; Figure S7; Data S4). These genes are enriched in
genetics. By the method of “pwild loquat/pcultivated loquat” with GO terms including the “Isopentenyl diphosphate biosyn-
95% confidence intervals, we identified 341 genomic blocks thetic process,” “Jasmonic acid biosynthetic process” and
holding 3041 putative protein-coding genes showing evi- “RNA process” of biological processes; “Golgi apparatus”
dence of selection sweeps. By combining FST outliers and and “Apoplast” of cellular components; and “Carboxylic
pwild loquat/pcultivated loquat” with the same standard, the corre- ester hydrolase” and “Xyloglucan: xyloglucosyl transferase
sponding numbers are narrowed to 39 and 347 respectively activity” of molecular functions (Figure S8; Data S4). KEGG
(Table 3; Figure S5; Data S4). These genes were enriched in analysis indicated that the protein-coding gene loci under-
Gene Ontology (GO) terms belonging to biological pro- gone balance selection were enriched in biosynthetic path-
cesses including “Alcohol metabolic process,” “Protein gly- ways including “glycolysis/Gluconeogenesis,” “Galactose
cosylation” and “Negative regulation of flower metabolism,” “Starch and sucrose metabolism,” “N-glu-
development;” cellular components including “Cytoskele- can metabolism” and “Amino sugar and nucleotide sugar
ton,” “Thylakoid membrane” and “Mitochondrial;” and metabolism” (Figure S8; Data S4). These results combined
molecular functions including “Flavin adenine dinucleotide with the forgoing selective sweep analysis suggested that
binding” and “catalytic activity” (Figure S6; Data S4). Kyoto genes related to saccharide metabolism were a focus of
Encyclopedia of Genes and Genomes (KEGG) analysis artificial selection, and different genes involved in the
showed that these genes were enriched in 50 pathways same metabolic pathway such as “Galactose metabolism”
including “Starch and sucrose metabolism,” “Galactose and “Starch and sucrose metabolism” were responsive
metabolism,” “Fructose and mannose metabolism” and during loquat domestication.
“Diterpenoid biosynthesis” (Figure S6; Data S4). These find- In total, the above results suggest that >10% of E. japon-
ings suggest that domestication and cultivation activities ica genes were affected by artificial selection, revealing the
had positive selection effects on genes related to the meta- extensive influence of domestication on the genetic back-
bolism of saccharides and diterpenoids, which endowed ground of cultivated E. japonica. However, when we fur-
loquat with important nutritional and medicinal value, ther improve the criteria for inferring selection effects to
respectively, and contributed to differentiation between wild 99% confidence intervals, by the method of “combining
and cultivated E. japonica. FST outlier and pwild loquat/pcultivated loquat,” only two genome
We also identified 216 and 63 genomic blocks of E. blocks on chromosome 11 including 11 genes showed evi-
japonica showing increased nucleotide polymorphism in dence of a selective sweep; and only six blocks showed
evidence of balancing the selection, including three hold-
ing 30 genes on chromosome 3, one holding six genes on
Table 3 Inferred numbers of genomic selective sweeps and genes chromosome 5 and one holding six genes on chromosome
under selection 8 (Table 3; Data S4).
P- No. of No. of Convergence and parallels in domestication of Rosaceae
Statistical methods value windows genes fruit crops
FST of cultivated loquat vs. wild ≤0.05 250 2530 Malus domestica and Prunus persica are important Rosa-
loquat
FST of cultivated loquat vs. wild ≤0.01 61 489
ceae fruit crops, for which evidence of selective sweeps
loquat (Duan et al., 2017; Yu et al., 2018) provide a good founda-
p of wild loquat divides cultivated ≤0.05 341 3673 tion to explore convergence and parallels with E. japonica
loquat domestication. To this end, we clustered gene families in
p of wild loquat divides cultivated ≤0.01 112 948 the three species, also determining chromosome colinear-
loquat
FST and p of wild loquat divides ≤0.05 39 347
ity of all putative protein-coding genes predicted in the
cultivated loquat three genomes. We identified 14 gene families, including
FST and p of wild loquat divides ≤0.01 2 11 those encoding “Glycosyltransferase” and “Transcription
cultivated loquat factor MYC2-like” in which genes showing selective
p of cultivated loquat divides wild ≤0.05 216 2014 sweeps among all three species co-clustered. Furthermore,
loquat
p of cultivated loquat divides wild ≤0.01 89 603
137, 259 and 125 families in which genes showing selective
loquat sweeps co-clustered, respectively, between E. japonica and
FST and p of cultivated loquat ≤0.05 63 450 M. domestica, between E. japonica and P. persica and
divides wild loquat between M. domestica and P. persica (Figure 2A; Data S5),
FST and p of cultivated loquat ≤0.01 6 43 suggesting convergent/parallel selection in the process of
divides wild loquat
domestication among or between these crops. We further

© 2021 Society for Experimental Biology and John Wiley & Sons Ltd,
The Plant Journal, (2021), doi: 10.1111/tpj.15209
6 Yunsheng Wang and Andrew H. Paterson
Figure 2. (a) Co-clustering gene family and (b) colinearity of orthologous genes located in selective sweep regions (indicated by green lines) of loquat and
apple; and loquat and peach.
used chromosome colinearity to identify 32 pairs of ortho-
logs or paralogs between E. japonica and M. domestica,
and four pairs between E. japonica and P. persica, located
in selective sweep regions of both genomes. Functional
annotation showed these orthologs between E. japonica and
M. domestica to encode proteins including a MADS-box
transcription factor (EVM0009815 vs. MDP0000366022) and
“UDP-glycosyltransferase 1” (EVM0043443 vs.
MDP0000875654), and these orthologs between E. japonica
and P. persica to encode proteins including “ABC transporter
protein” (EVM0035107 vs. Prupe.5G188500) and “signal
recognition particle 54 kDa protein (SRP-54)” (EVM0021037
vs. Prupe.7G104500) (Figure 2B; Data S6). In plants, MADS-
box transcription factors play key roles in regulating repro-
ductive growth including floral organ conformation, flower-
ing time and fruit development (Wang et al., 2017). UDP
glycosyltransferase 1 is responsible for transferring sugar
moieties to a diverse array of small molecules from activated
sugar donors, and playing key roles in controlling multiple
growth and development processes (Li et al., 2014). ABC
transporter proteins act as ATP-driven pumps to translocate
a wide range of substrates across membranes (Rees et al.,
2009). SRP-54 plays an important role in the routing of newly
synthesized proteins into the secretory pathway by interact-
ing with the signal peptide of secreted proteins (Lindstrom
et al., 1993). In partial summary, a small number of genes
show convergent and parallel selection in selective sweeps
between E. japonica and P. persica or M. domestica based
on the combination of gene family co-clustering and chro-
mosome colinearity.
DISCUSSION
By virtue of ripening in spring–early summer, E. japonica
fills a gap in the world’s “fruit basket,” and is of increasing
importance (Janick et al., 2015). To respond to this trend,
invigorated breeding progress is urgent, and genomic
knowledge of existing germplasm is a potentially great
asset. Notwithstanding the substantial improvement in fruit
size and taste of cultivated loquat but insufficient
© 2021 Society for Experimental Biology and John Wiley & Sons Ltd,
morphological differences to separate it clearly from its
direct wild progenitor render it “semi-domesticated”
according to the definition proposed by Meyer et al (2012).
As an intermediate toward domestication, the semi-domes-
ticated crop could provide unique insight into the domesti-
cation process, with incipient morphological and genetic
differentiation from its wild progenitor.
Here, levels and patterns of genome-wide diversity cou-
pled with biogeographic data suggest a possible path for
the origin and domestication of E. japonica. The south-
west part of Guizhou province is suspected to be the birth-
place or refuge of E. japonica species in the last glacial
maximum. The initial wild E. japonica population
expanded out to a wider range, still surviving in Guizhou
province and surrounding mountainous regions such as
the north-west portions of Hunan and Yunnan provinces,
as well as south-east Sichuan and Chongqing provinces,
and western Hubei province. About 2000 years ago in the
Han dynasty, people in the transition zone from the moun-
tains to the hilly plain of Yichang city in north-west Hubei
province, began to plant wild E. japonica from nearby
mountains, undertaking “primary” domestication. The
primitive cultivated E. japonica then diffused to suitable
growth areas of China, mainly in the middle and lower
reaches of the Yangtze River and the southern region. Still
in a semi-wild state with an acid taste, primitive cultivated
E. japonica trees remain scattered widely in southern
China. However, people in southern Jiangsu, Zhejiang and
Fujian provinces, a region with a rich economy and devel-
oped agriculture, undertook breeding activities that
resulted in delicious E. japonica varieties of commercial
value, that were more widely cultivated and introduced to
Japan, Europe, the United States and other countries (Lin
et al., 1999). Thus, E. japonica appears to exemplify a typi-
cal, albeit rare, case of the “marginality model,” which
assumes that domestication is often driven by reproductive
isolation from wild forms due to the removal of plants
from their native range (Meyer et al., 2012; Verhoeven,
2004).
The Plant Journal, (2021), doi: 10.1111/tpj.15209

Complementing genome-wide diversity, levels and pat-
terns of diversity in individual genes and their relation-
ships to morphological and physiological variation provide
insight into the identities of “domestication genes.” By
high-throughput whole genome re-sequencing, here we
identified candidate genes showing “footprints” of
response to artificial selection during the process of
domestication. While such analyses are associated with a
wide range of possible spurious outcomes, the populations
of genes we have identified provide a starting point for
more detailed genetic and/or functional studies to evaluate
their roles (if any) in economic traits.
Crops differ widely in botanical classification, geographi-
cal distribution and domestication processes. However,
their “domestication syndrome” often has high consis-
tency, particularly among closely related plants cultivated
for similar purposes. Logically, such “convergent” or “par-
allel” domestication leading to similar or identical pheno-
types would be determined by genes encoding similar
proteins and having similar biological function in different
crops. Tracking these genes has become a new interesting
issue for geneticists and botanists (Rendo
n-Anaya and Her-
rera-Estrella, 2018). For example, a dormancy gene in soy-
bean, rice and tomato (Wang et al., 2018), a shattering
gene in cereals (Lin et al., 2012) and a flowering time gene
in cereals (Liu et al., 2015) have been identified as experi-
encing parallel artificial selection. High-throughput
sequencing, combining expression quantitative trait loci
and metabolome-based genome-wide association studies
(Zhu et al., 2018), or combining genome-wide association
studies (Tao et al., 2017) have also been used to search for
genes responsible for parallel artificial selection. While
exceptions to convergent domestication have been
reported (Tang et al., 2013), even by advocates (Paterson
et al., 1995), there is still appreciable merit in exploring for
related gene functions in divergent taxa. While we found
few cases including genes coding “UDP glycosyltrans-
ferase 1” among loquat, apple and peach studied here,
coupling of co-clustering analysis for gene families and
chromosome colinearity analysis for selective sweep
orthologs between species are promising approaches that
warrant further investigation to identify genes consistent
with parallel and convergent artificial selection at the
whole genome level. This result also provides evidence
that parallel/convergent selective sweeps among different
crops may not be very extensive.
EXPERIMENTAL PROCEDURES
Sampling for re-sequencing
In total, 51 accessions wild E. japonica collected from 51 counties
of six provinces including Guizhou (22), Hunan (six), Hubei (10),
Yunnan (one), Chongqing (eight), Sichuan (three) and Shaanxi
(one) represented the species range distribution of wild loquat,
© 2021 Society for Experimental Biology and John Wiley & Sons Ltd,
The Plant Journal, (2021), doi: 10.1111/tpj.15209
Population genomics of loquat 7
while 52 accessions represented cultivated loquat populations
bred in China (46), Japan (one), America (one) and Europe (five).
The information about the geographical origin of wild loquat sam-
ples and cultivated loquat varieties were listed in Data S1, and the
specimens were kept at Kaili University.
DNA extraction
Total genomic DNA was extracted from young leaves of the “Big
Five-point Star” by using a modified protocol based on the CTAB
method (Doyle and Doyle, 1987), then RNAse was used to remove
RNA contamination from DNA in a water bath at 37°C for 1 h. The
quality of and content of total genomic DNA were checked by using
agarose gel electrophoresis and spectrophotometry (NanoDrop
WND-1000; NanoDrop Technologies Inc., Wilmington, DE, USA).
Only extracted DNA with concentration >50 ng/ll, OD260/280
between 1.8 and 2.0, OD260/OD230 between 1.6 and 1.8, and total
content >5 lg were used for the construction of sequencing
libraries.
Illumina short-read library construction, sequencing and
raw data statistics
Illumina paired-end read libraries (350 bp) were constructed strictly
according to the guideline of sequencer manufacturer as following
steps: DNA was fragmented by using the E210 Covaris instrument
(Covaris, Inc., Woburn, MA, USA) and fragments of about 350 bp
length were selected on 3% agarose gel; selected DNA fragments
were then end-repaired, A-tailed and Illumina compatible adaptors
(BioScientific, Austin, TX, USA) ligated by using the SPRIWorks
Library Preparation System and SPRI TE instrument (Beckmann
Coulter, Fullerton, CA, USA), then were polymerase chain reaction-
amplified by using Illumina adapter-specific primers and Platinum
Pfx DNA polymerase (Invitrogen, Carlsbad, CA, USA); quality and
quantity of sequencing libraries were checked by using the Agilent
2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) and
quantitative polymerase chain reaction using the KAPA Library
Quantification Kit (Kapa Biosystems, Wilmington, MA, USA) on a
MxPro instrument (Agilent Technologies) respectively. After that,
paired-end read libraries were sequenced using Illumina HiSeq 4000
(Illumina, San Diego, CA, USA).
Data mapping and SNP calling
The raw short reads were filtered to remove the sequencing adap-
tor as well as reads with N content >10% and quality value of 50%
bases <10. The remaining clean short reads were mapped to
assemble a reference genome of the “Big Five-pointed Star” by
using software BWA (Li and Durbin, 2009). Its whole genome
sequence and the protein-coding genes sequences have been
deposited in China National Center for Bioinformation (https://
bigd.big.ac.cn/gwh: WGS010381) (Wang, 2021). After mapping of
clean reads to the assembled reference genome, the program
Picard (http://sourceforge.net/projects/picard/) was executed to fil-
ter redundant reads (MarkDuplicates). Finally, the HaplotypeCaller
algorithm built into software toolkit GATK (McKenna et al., 2010)
was performed to detect SNPs and small insertions and deletions
of small fragments following parameter settings: (i) Clustersize: 2;
Clusterwindowsize: 5 (indicating that the number of variations in
the 5 bp window should not exceed 2); (ii) QUAL:30 (the mutant
loci with sequencing quality value <30 are filtered out – the quality
value of 30, indicating the sequencing accuracy of a base is 99.9%
according to the phred format); (iii) QD <2.0 was filtered out (QD
means the ratio of the quality value vs. the coverage depth of the
mutant loci); (iv) MQ <40 is filtered out (all the root-mean-square
8 Yunsheng Wang and Andrew H. Paterson
of the comparison-quality value to read on that bit); (v) FisherS-
trand notation (FS) >60 is filtered out (FS is the value converted
from P-value of the Fisher exact test, describing whether a clear
positive or negative chain specificity existed in the reads only with
variant or only matching the reference sequence, in the process of
sequencing or alignment – with no strain-specific aligning result,
FS should be close to 0); and (vi) remaining filtering parameters
for mutant loci were handled by default values specified by GATK,
obtaining an initial SNP data set among sequencing samples.
Finally, we further filtered the initial SNP dataset according to the
criterion of site integrity ≥0.8 and minor allele frequent ≥0.05, and
the remaining SNP dataset was used for downstream analyses.
Phylogenetic tree construction of loquat samples
The neighbor-joining method built into program MEGA5 (Tamura
et al., 2011) was used to construct the phylogenetic tree of 104 cul-
tivated and wild loquat accessions by setting the nucleotide sub-
stitute model as Kimura 2-parameter and bootstrap as 1000.
Population structure analysis
Population genetic structure refers to a non-random distribution of
genetic variation in a species or population. According to geographi-
cal distribution or other criteria, a population can be divided into sev-
eral subgroups. Individuals in the same subgroup have closer genetic
relationships, and in different subgroups have more distant relation-
ships. Population structure analysis can estimate the number of
ancestors of the studied population and infer the origin of each sam-
ple. At present, it is a popular method of population clustering analy-
sis, which is helpful to understand the evolution of materials. In this
paper, we used the software ADMIXTURE (Alexander et al., 2009) to evalu-
ate population structure. ADMIXTURE software calculates the optimal K
value (the number of subgroup) by calculating the error rate of cross-
validation, the optimal K value corresponding to the lowest error rate
calculated by crossing-validation, and ultimately determining the opti-
mal number of subpopulations in the group.
Evaluation of genetic diversity
The nucleotide polymorphism: p (Tajima, 1983) and h (Watterson,
1975), Neutral test: Tajima’s test (Tajima, 1989) and Fu and Li’s
test (Fu and Li, 1993) of the cultivated and wild loquat populations,
and the genetic differentiation (Wright, 1949) (FST, a standardized
measure of the variance of allele frequencies among populations
between these two population were evaluated based on the SNP
data by the software POPGENOME (Pfeifer et al., 2014) in the R pack-
age (https://www.r-project.org/).
Gene flow between wild and cultivated loquat
populations
The program MIGRATE, v.0.3 built in LAMARC software package (http://
evolution.genetics.washington.edu/lamarc/lamarc_download.
html), was used to simulate the gene flow between wild and the cul-
tivated loquat, and effective population size of both populations
with four models (model 1: two-way gene flow exists between the
wild and the cultivated loquat population; model 2: gene flow from
the wild into the cultivated loquat population; model 3: gene flow
from the cultivated into the wild loquat population; model 4: no
gene flow between the wild and the cultivated loquat population).
Recombination and LD
The population-scaled recombination rates (q = 4Ner) (Ne = effec-
tive population size) and LD level of the cultivated, wild and com-
plex loquat populations were calculated by software HAPLOVIEW
© 2021 Society for Experimental Biology and John Wiley & Sons Ltd,
(Barrett, 2009) using standard methods (International HapMap
Consortium, 2005; McVean et al., 2004).
Demography dynamics of wild and cultivated loquat
population
The program SMC++ (https://github.com/popgenmethods/smcpp)
was used to simulate the demography dynamics of wild and culti-
vated loquat populations with parameter setting as the core
mutant rate (base substitute rate) = 5e-9 and generation
time = 10 years.
Identification of selection effect of genome blocks and
genes
Three methods were used to detect selective sweeps in genomic
sequence. The first one is the FST outlier approach (Beaumont,
2005) using the program BAYESCAN (http://cmpg.unibe.ch/software/
BayeScan/) in the multinomial-Dirichlet mode. The FST outlier
approach is to detect variable positions that exhibit significantly
more or less than average differentiation between the wild and
the cultivated loquat populations, suggesting candidate gene
regions that have been affected by selection. The second method
is the nucleotide polymorphism (p) approach (Luikart et al., 2003;
Schlo€ tterer, 2003), identifying genomic regions where the nucleo-
tide diversity of pwild/p cultivated is reduced sharply, the top 5% or
1% being defined as selective sweeps. The third method is com-
bining the FST-p approaches (Akey et al., 2002; Storz, 2005).
The above methods were all based on all SNP loci of a specific
step length (such as 10 kb) in sliding windows (such as 100 kb).
For species without reference genomes, a SLAF label can be used
as a sliding window to calculate selective sweeps. The method of
detecting selective sweep regions in the whole genome is to cal-
culate population genetic indices such as population differentia-
tion index (FST), nucleotide polymorphism (Pi), Tajima’s D and so
on, of all SNP loci in a sliding window (such as 100 kb) with a
specific step size (such as 10 kb), and to judge whether a particu-
lar window is selected according to the calculated results. The
genes located in salient genomic blocks were identified and fur-
ther annotated by using BLASTX (E value < 1.0 E 5) against the
databases of Nr (Marchler-Bauer et al., 2011), TrEMBL (Boeck-
mann et al., 2003), GO (Dimmer et al., 2012), COG (Tatusov et al.,
2000) and KEGG (Kanehisa et al., 2004). We also performed GO
enrichment analysis by using software GOseq (Young et al., 2010)
and KEGG enrichment analysis by using software KOBAS (Mao
et al., 2005) respectively.
Gene families clustering and colinearity among Eriobotrya
japonica, Malus domestica and Prunus persica
The Generic Feature Format Version 3 (gff3) data file of M. domes-
tica (https://www.rosaceae.org/species/malus/malus_x_domestica/
genome_v1.0), P. persica (https://www.rosaceae.org/species/pru
nus_persica/genome_v1.0) and E. japonica genome (https://bigd.b
ig.ac.cn/?lang=zh; GWHAOQU00000000) were used to analysis the
clustering of the gene families and colinearity among above three
species. First, we filtered the genes with 150 nucleotides, then con-
verted to coding sequence alignments by using REVTRANS 1.4 (Wern-
ersson and Pedersen, 2003). After that, we aligned the protein
sequences of filtered gene sets of E. japonica, M. domestica and P.
persica, with E ≤ 1E5 and the number of hits ≤500 by using all-
against-all BLASTP (Altschul et al., 1997). Finally, we analyzed align-
ment results by using ORTHOMCL (Li et al., 2003) software with MCL
inflation parameter set at 1.5 to categorize the gene families of the
three species.
The Plant Journal, (2021), doi: 10.1111/tpj.15209

We identified inter-synteny among genomes of E. japonica, M.
domestica and P. persica based on all-against-all BLASTP results
by using MCScan (Wang et al., 2012). A genome region containing
10–25 genes in the identified gene pairs was regarded as syntenic,
and we aligned the protein sequences of homologous gene pairs
(by using by MUSCLE v3.8.31 software) in the identified syntenic
regions with the following parameters: MATCH_SCORE, 50;
MATCH_SIZE, 5; GAP_PENALTY, 1; OVERLAP_WINDOW, 5;
E_VALUE, 1e-05; MAX GAPS, 25 (Edgar, 2004).
Identification of parallel molecular clues of positive
selection for domestication in Malus domestica and
Prunus persica
Genes of M. domestica and P. persica located in genomic regions
with selective sweeps have been identified by Duan et al. (2017:
https://doi.org/10.1038/s41467-017-00336-7: “Supplementary data
6: 41467_2017_336_MOESM7_ESM” and “Supplementary data 8:
41467_2017_336_MOESM9_ESM”), and Yu et al. (2018: (https://doi.
org/10.1038/s41467-018-07744-3: “Supplementary data 8:
41467_2018_7744_MOESM12_ESM”). Based on the analysis of
gene families clustered and colinear among E. japonica, M.
domestica and P. persica, we identified orthologous and paralo-
gous genes both experiencing selective sweeps between E. japon-
ica and M. domestica; and E. japonica and P. persica.
ACKNOWLEDGMENTS
This work was funded by the National Natural Science Foundation
of China (31560091), key project of the Science Department of
Guizhou Province [LH(2015)7754], and Science and technology
plan project of Guizhou Province [2019]4318. We really appreci-
ated Professor Lin Shunquan (School of horticulture Science,
South China Agricultural University) for providing samples of
loquat cultivars. AHP appreciates an Adjunct Professorship at
SWU, and visiting scientist appointment at NCUST. We sincerely
thank the experimental personnel and bioinformatics analysts in
Biomarker company (www.biomarker.com.cn) who participated in
this project.
AUTHOR CONTRIBUTIONS
YSW designed the experiments, collected samples, ana-
lyzed data and wrote the paper; YSW and AHP and wrote
the paper.
CONFLICT OF INTERESTS
The authors declare that they have no competing interests
DATA AVAILABILITY STATEMENT
The raw sequencing data of 103 loquat accessions have
been deposited in China National Center for Bioinforma-
tion and can be found by hyperlinking to the website:
https://bigd.big.ac.cn/search/?dbId=&q=+CRA003201.
SUPPORTING INFORMATION
Additional Supporting Information may be found in the online ver-
sion of this article.
Figure S1. Display of geographical distribution, sampling and
domestication of common loquat.
Figure S2. LD level of genome and chromosomes of cultivated
and wild loquat populations.
© 2021 Society for Experimental Biology and John Wiley & Sons Ltd,
The Plant Journal, (2021), doi: 10.1111/tpj.15209
Population genomics of loquat 9
Figure S3. Demographical dynamics simulation of cultivated and
wild loquat populations (nucleotide substitute rate of per year per
generation is set as 5910-9, the generation age is set as ten years)
Figure S4. Population structure of 104 common loquat accessions
with admixture models
Figure S5. Genes in loquat genome regions undergone selection
sweep
Figure S6. GO and KEGG enrichment statistics of genes under-
gone selection sweep by Pi of wild/cultivated & FST measure
Figure S7. Genes undergone balance selection
Figure S8. GO and KEGG enrichment statistics of genes under-
gone balance selection by Pi of cultivated/wild & FST measure
Data S1. Sampling geographical information of wild and culti-
vated loquat accesions;
Data S2. Statistics of clean sequencing data of 104 accessions
loquat
Data S3. Demographic dynamics in the evolution history of wild
and cultivated loquat population
Data S4. Summary of selection effect genes in loquat genome
Data S5. Gene family clustering of selection sweep genes among
loquat, apple and peach
Data S6. Co-selection sweeping between loquat and apple, and
loquat and peach
REFERENCES
Akey, J.M., Zhang, G., Zhang, K., Jin, L. & Shriver, M.D. (2002) Interrogating
a high-density SNP map for signatures of natural selection. Genome
Research, 12, 1805–1814. https://doi.org/10.1101/gr.631202.
Alexander, D.H., Novembre, J. & Lange, K. (2009) Fast model-based estima-
tion of ancestry in unrelated individuals. Genome Research, 19, 1655–
1664. https://doi.org/10.1101/gr.094052.109.
Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J.H., Zhang, Z., Miller,
W. & et al. (1997) Gapped BLAST and PSI-BLAST: A new generation of
protein database search programs. Nucleic Acids Research, 25, 3389–
3402. https://doi.org/10.1093/nar/25.17.3389.
Badenes, M.L., Blasco, M. & Naval, M.M. (2015) Loquat: Progress and
expectations. Acta Horticulture, 1092, 19–24. https://doi.org/10.17660/Acta
Hortic.2015.1092.1.
Barrett, J.C. (2009) Haploview: Visualization and analysis of SNP genotype
data. Cold Spring Harbor Protocols, 2009(10), pdb.ip71. https://doi.org/10.
1101/pdb.ip71.
Beaumont, M.A. (2005) Adaptation and speciation: What can FST tell us?
Trends in Ecology & Evolution, 20, 435–440. https://doi.org/10.1016/j.tree.
2005.05.017.
Boeckmann, B., Bairoch, A., Apweiler, R., Blatter, M.C., Estreicher, A., Gas-
teiger, E. et al. (2003) The SWISS-PROT protein knowledgebase and its
supplement TrEMBL in 2003. Nucleic Acids Research, 31, 365–370.
https://doi.org/10.1093/nar/gkg095.
Cao, K., Li, Y., Deng, C.H., Gardiner, S.E., Zhu, G., Fang, W. et al. (2019)
Comparative population genomics identified genomic regions and candi-
date genes associated with fruit domestication traits in peach. Plant
Biotechnology Journal, 17, 1954–1970. https://doi.org/10.1111/pbi.13112.
Cao, K., Zheng, Z., Wang, L., Liu, X., Zhu, G., Fang, W. et al. (2014) Compar-
ative population genomics reveals the domestication history of the
peach, Prunus persica, and human influences on perennial fruit crops.
Genome Biology, 15, 415. https://doi.org/10.1186/s13059-014-0415-1.
Cornille, A., Gladieux, P. & Giraud, T. (2013) Crop-to-wild gene flow and spa-
tial genetic structure in the closest wild relatives of the cultivated apple.
Evolutionary Applications, 6, 737–748. https://doi.org/10.1111/eva.12059.
Cornille, A., Gladieux, P., Smulders, M.J.M., Rolda
n-Ruiz, I., Laurens, F., Le
Cam, B. et al. (2012) New insight into the history of domesticated apple:
Secondary contribution of the European wild apple to the genome of cul-
tivated varieties. PLoS Genetics, 8, e1002703. https://doi.org/10.1371/
journal.pgen.1002703.
Dimmer, E.C., Huntley, R.P., Alam-Faruque, Y., Sawford, T., O’Donovan, C.,
Martin, M.J. et al. (2012) The UniProt-GO annotation database in 2011.
10 Yunsheng Wang and Andrew H. Paterson
Nucleic Acids Research, 40, D565–D570. https://doi.org/10.1093/nar/
gkr1048.
Dirzo, R. & Raven, P.H. (2003) Global state of biodiversity and loss. Annual
Review of Environment and Resources, 28, 137–167.
Doyle, J.J. & Doyle, J.L. (1987) A rapid DNA isolation procedure for small
quantities of fresh leaf tissue. Phytochemical Bulletin, 19, 11–15.
Duan, N., Bai, Y., Sun, H. et al. (2017) Genome re-sequencing reveals the
history of apple and supports a two-stage model for fruit enlargement.
Nature Communications, 8, 249. https://doi.org/10.1038/s41467-017-
00336-7.
Edgar, R.C. (2004) MUSCLE: Multiple sequence alignment with high accu-
racy and high throughput. Nucleic Acids Research, 32, 1792–1797.
https://doi.org/10.1093/nar/gkh340.
Feurtey, A., Cornille, A., Shykoff, J.A., Snirc, A. & Giraud, T. (2016) Crop-to-
wild gene flow and its fitness consequences for a wild fruit tree: towards
a comprehensive conservation strategy of the wild apple in Europe. Evo-
lutionary Applications, 10(2), 180–188. https://doi.org/10.1111/eva.12441.
Fu, Y.X. & Li, W.H. (1993) Statistical tests of neutrality of mutations. Genet-
ics, 133, 693–709.
Gepts, P. (2004) Crop domestication as a long-term selection experiment.
Plant Breeding Reviews, 24, 1–44. https://doi.org/10.1002/
9780470650288.ch1.
Guo, S., Zhao, S., Sun, H., Wang, X., Wu, S., Lin, T. et al. (2019) Resequenc-
ing of 414 cultivated and wild watermelon accessions identifies selection
for fruit quality traits. Nature Genetics, 51, 1616–1623. https://doi.org/10.
1038/s41588-019-0518-4.
Harlan, J.R. (1992) Crops and Man. Madison, WI, USA: American Society of
Agronomy and Crop Science Society of America.
Hazzouri, K.M., Flowers, J., Visser, H.J., Khierallah, H.S.M., Rosas, U.,
Pham, G.M. et al. (2015) Whole genome re-sequencing of date palms
yields insights into diversification of a fruit tree crop. Nature Communi-
cations, 6, 8824. https://doi.org/10.1038/ncomms9824.
Huang, X., Kurata, N., Wei, X., Wang, Z.-X., Wang, A., Zhao, Q. et al. (2012)
A map of rice genome variation reveals the origin of cultivated rice. Nat-
ure, 490, 497–501. https://doi.org/10.1038/nature11532.
Hufford, M.B., Xu, X., van Heerwaarden, V., Pyha€ ja€rvi, T., Chia, J.-M., Cart-
wright, R.A. et al. (2012) Comparative population genomics of maize
domestication and improvement. Nature Genetics, 44, 808–811. https://
doi.org/10.1038/ng.2309.
International HapMap Consortium. (2005) A haplotype map of the human
genome. Nature, 437, 1299–1320. https://doi.org/10.1038/nature04226.
Janick, J., Zhang, Z. & Lin, S. (2015) Important world cultivars of loquat.
Acta Horticulturae, 1092, 25–32. https://doi.org/10.17660/ActaHortic.2015.
1092.2
Kanehisa, M., Araki, M., Goto, S., Hattori, M., Hirakawa, M., Itoh, M., et al.
(2004) The KEGG resource for deciphering the genome. Nucleic Acids
Research, 32, D277–D280.
Kawuki, R.S., Ferguson, M., Labuschagne, M., Herselman, L. & Kim, D.J.
(2009) Identification, characterisation and application of single nucleotide
polymorphisms for diversity assessment in cassava (Manihot esculenta
Crantz). Molecular Breeding, 23, 669–684. https://doi.org/10.1007/s11032-
009-9264-0.
Li, H. & Durbin, R. (2009) Fast and accurate short read alignment with Bur-
rows-Wheeler transform. Bioinformatics, 25, 1754–1760. https://doi.org/
10.1093/bioinformatics/btp324.
Li, L., Stoeckert, C.J. & Roos, D.S. (2003) OrthoMCL: Identification of ortho-
log groups for eukaryotic genomes. Genome Research, 13, 2178–2189.
https://doi.org/10.1101/gr.1224503.
Li, Y., Li, P., Wang, Y. & Dong, R. (2014) Genome-wide identification and
phylogenetic analysis of Family-1 UDP glycosyltransferases in maize
(Zea mays). Planta, 239, 1265–1279. https://doi.org/10.1007/s00425-014-
2050-1.
Lin, S.Q., Sharpe, R.H. & Janick, J. (1999) Loquat: Botany and horticulture.
Horticultural Reviews, 23, 233–276. https://doi.org/10.1002/
9780470650752.ch5.
Lin, S., Yang, X.H., Liu, C.M., Hu, Y.L. & Liu, Z.L. (2004) Natural geographical
distribution of genus Eriobotrya plants in China. Acta Horticulturae
Sinica, 31, 569–573.
Lin, T., Zhu, G., Zhang, J. et al. (2014) Genomic analyses provide insights
into the history of tomato breeding. Nature Genetics, 46, 1220–1226.
https://doi.org/10.1038/ng.3117.
© 2021 Society for Experimental Biology and John Wiley & Sons Ltd,
Lin, Z., Li, X., Shannon, L.M., Yeh, C.T. et al. (2012) Parallel domestication of
the Shattering1 genes in cereals. Nature Genetics, 44, 720–724. https://
doi.org/10.1038/ng.2281.
Lindstrom, J.T., Chu, B. & Belanger, F.C. (1993) Isolation and characteriza-
tion of an Arabidopsis thaliana gene for the 54 kDa subunit of the signal
recognition particle. Plant Molecular Biology, 23, 1265–1272. https://doi.
org/10.1007/BF00042359.
Liu, H., Liu, H., Zhou, L., Zhang, Z., Zhang, X., Wang, M. et al. (2015)
Parallel domestication of the heading date 1 gene in cereals. Molecu-
lar Biology and Evolution, 32, 2726–2737. https://doi.org/10.1093/molbe
v/msv148.
Luikart, G., England, P.R., Tallmon, D., Jordon, S. & Taberlet, P. (2003) The
power and promise of population genomics: From genotyping to gen-
ome typing. Nature Reviews Genetics, 4, 981–994. https://doi.org/10.
1038/nrg1226.
Mao, X., Cai, T., Olyarchuk, J.G. & Wei, L.J.B. (2005) Automated genome
annotation and pathway identification using the KEGG Orthology (KO) as
a controlled vocabulary. Bioinformatics, 21, 3787–3793. https://doi.org/10.
1186/s12870-020-02553-7.
Marchler-Bauer, A., Lu, S., Anderson, J.B., Chitsaz, F., Derbyshire, M.K.,
DeWeese-Scott, C. et al. (2011) CDD: A conserved domain database for
the functional annotation of proteins. Nucleic Acids Research, 39, D225–
D229. https://doi.org/10.1093/nar/gkq1189.
Matsuoka, Y., Vigouroux, Y., Goodman, M.M., Sanchez, J., Buckler, E. &
Doebley, J. (2002) A single domestication for maize shown by multilocus
microsatellite genotyping. Proceedings of the National Academy of
Sciences, 99, 6080–6084. https://doi.org/10.1073/pnas.052125199.
McKenna, A., Hanna, M., Banks, E., Sivachenko, A., Cibulskis, K., Kernytsky,
A. et al. (2010) The Genome Analysis Toolkit: A MapReduce framework
for analyzing next-generation DNA sequencing data. Genome Research,
20, 1297–1303. https://doi.org/10.1101/gr.107524.110.
McVean, G.A., Myers, S.M., Hunt, S., Deloukas, P., Bentley, D.R. & Donnelly,
P. (2004) The fine-scale structure of recombination rate variation in the
human genome. Science, 304, 581–584. https://doi.org/10.1126/science.
1092500.
Meyer, R.S., DuVa, A.E. & Jensen, H.R. (2012) Patterns and processes in
crop domestication: An historical review and quantitative analysis of 203
global food crops. New Phytologist, 196, 29–48. https://doi.org/10.1111/j.
1469-8137.2012.04253.x.
Miller, A.J. & Gross, B.L. (2011) From forest to field: Perennial fruit crop
domestication. American Journal of Botany, 98, 1389–1414. https://doi.
org/10.3732/ajb.1000522.
Morrell, P.L., Buckler, E.S. & Ross-Ibarra, J. (2012) Crop genomics:
Advances and applications. Nature Reviews Genetics, 13, 85–96. https://
doi.org/10.1038/nrg3097.
Olsen, K.M. & Wendel, J.F. (2013) A bountiful harvest: Genomic insights
into crop domestication phenotypes. Annual Review of Plant Biology, 64,
47–70. https://doi.org/10.1146/annurev-arplant-050312-120048.
Paterson, A.H., Lin, Y.R., Li, Z., Schertz, K.F., Doebley, J.F., Pinson, S.R.
et al. (1995) Convergent domestication of cereal crops by independent
mutations at corresponding genetic loci. Science, 269, 1714–1718. https://
doi.org/10.1126/science.269.5231.1714.
Pfeifer, B., Wittelsburger, U., Ramos-Onsins, S.E. & Lercher, M.J. (2014)
PopGenome: An efficient Swiss army knife for population genomic anal-
yses in R. Molecular Biology and Evolution, 31, 1929–1936. https://doi.
org/10.1093/molbev/msu136.
Pickersgill, B. (2007) Domestication of plants in the Americas: Insights from
Mendelian and molecular genetics. Annals of Botany, 100, 925–940.
https://doi.org/10.1093/aob/mcm193.
Purugganan, M.D. & Fuller, D.Q. (2009) The nature of selection during plant
domestication. Nature, 457, 843–848. https://doi.org/10.1038/nature07895.
Qi, J.J., Liu, X., Sato, S., Miao, H., Xie, B., Li, X. et al. (2013) A genomic vari-
ation map provides insights into the genetic basis of cucumber domesti-
cation and diversity. Nature Genetics, 45, 1510–1518. https://doi.org/10.
1038/ng.2801.
Rees, D.C., Johnson, E. & Lewinson, O. (2009) ABC transporters: The power
to change. Nature Reviews Molecular Cell Biology, 10, 218–227. https://
doi.org/10.1038/nrm2646.
Rendo
n-Anaya, M. & Herrera-Estrella, A. (2018) The advantage of parallel
selection of domestication genes to accelerate crop improvement. Gen-
ome Biology, 19, 147. https://doi.org/10.1186/s13059-018-1537-7.
The Plant Journal, (2021), doi: 10.1111/tpj.15209

Rubin, C.J., Zody, M.C., Meadows, J.R.S., Sherwood, E., Webster, M.T.,
Jiang, L. et al. (2010) Whole-genome resequencing reveals loci under
selection during chicken domestication. Nature, 464, 587–591. https://doi.
org/10.1038/nature08832.
Schlo€ tterer, C. (2003) Hitchhiking mapping–functional genomics from the
population genetics perspective. Trends in Genetics, 19, 32–38. .https://
doi.org/10.1016/s0168-9525(02)00012-4.
Schmutz, J., Mamidi, P.E., Wu, S. et al. (2014) A reference genome for com-
mon bean and genome-wide analysis of dual domestications. Nature
Genetics, 46, 707–713. https://doi.org/10.1038/ng.3008.
Schmutz, J., McClean, P.E., Mamidi, S., Wu, G.A., Cannon, S.B., Grimwood,
J. et al. (2018) Genomic approaches for studying crop evolution. Gen-
ome Biology, 19, 140. https://doi.org/10.1186/s13059-018-1528-8.
Storz, J.F. (2005) INVITED REVIEW: Using genome scans of DNA polymor-
phism to infer adaptive population divergence. Molecular Ecology, 14,
671–688. https://doi.org/10.1111/j.1365-294X.2005.02437.x.
Tajima, F. (1983) Evolutionary relationship of DNA sequences in finite popu-
lations. Genetics, 105, 437–460.
Tajima, F. (1989) Statistical method for testing the neutral mutation hypoth-
esis by DNA polymorphism. Genetics, 123, 585–595.
Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M. & Kumar, S.
(2011) MEGA5: Molecular evolutionary genetics analysis using maximum
likelihood, evolutionary distance, and maximum parsimony methods.
Molecular Biology and Evolution, 28, 2731–2739. https://doi.org/10.1093/
molbev/msr121.
Tang, H., Cuevas, H.E., Das, S., Sezen, U.U., Zhou, C., Guo, H. et al. (2013)
Seed shattering in a wild sorghum is conferred by a locus unrelated to
domestication. Proceedings of the National Academy of Sciences, 110,
15824–15829. https://doi.org/10.1073/pnas.1305213110
Tao, Y., Mace, E.S., Tai, S., Cruickshank, A., Campbell, B.C., Zhao, X.
et al. (2017) Whole-genome analysis of candidate genes associated
with seed size and weight in Sorghum bicolor reveals signatures of
artificial selection and insights into parallel domestication in cereal
crops. Frontiers in Plant Science, 8, 123. https://doi.org/10.3389/fpls.
2017.01237.
Tatusov, R.L., Natale, D.A., Garkavtsev, I.V., Tatusova, T.A., Shankavaram,
U.T., Rao, B.S. et al. (2001) The COG database: New developments in
phylogenetic classification of proteins from complete genomes. Nucleic
Acids Research, 29, 22–28. https://doi.org/10.1093/nar/29.1.22.
Verhoeven, M. (2004) Beyond boundaries: Nature, culture, and a holistic
approach to domestication in the Levant. Journal of World Prehistory,
18, 179–282. https://doi.org/10.1007/s10963-004-4361-9.
Wang, M., Li, W., Fang, C., Xu, F., Liu, Y., Wang, Z. et al. (2018) Parallel
domestication of a dormancy gene in crops from multiple families. Nat-
ure Genetics, 50, 1435–1441. https://doi.org/10.1038/s41588-018-0229-2.
Wang, Y. (2021) A draft genome at chromosome level and metabolomes of
leave, root and flowers provide insights into the molecular basis of
© 2021 Society for Experimental Biology and John Wiley & Sons Ltd,
The Plant Journal, (2021), doi: 10.1111/tpj.15209
View publication stats
Population genomics of loquat 11
medicinal ingredients of loquat (Eriobotrya japonica sp;(Thunb.) Lindl).
https://doi.org/10.21203/rs.3.rs-150389/v1
Wang, Y., Shahid, M.Q., Lin, S., Chen, C. & Hu, C. (2017) Footprints of
domestication revealed by RAD-tag resequencing in loquat: SNP data
reveals a non-significant domestication bottleneck and a single domesti-
cation event. BMC Genomics, 18, 354. https://doi.org/10.1186/s12864-017-
3738-y.
Wang, Y., Tang, H., DeBarry, J.D., Tan, X., Li, J. & Wang, X. et al. (2012)
MCScanX: A toolkit for detection and evolutionary analysis of gene syn-
teny and colinearity. Nucleic Acids Research, 40, e49. https://doi.org/10.
1093/nar/gkr1293.
Watterson, G.A. (1975) On the number of segregating sites in genetical
models without recombination. Theoretical Population Biology, 7, 256–
276. https://doi.org/10.1016/0040-5809(75)90020-9.
Wernersson, R. & Pedersen, A.G. (2003) RevTrans: Multiple alignment of
coding DNA from aligned amino acid sequences. Nucleic Acids
Research, 31, 3537–3539. https://doi.org/10.1093/nar/gkg609.
Wright, S. (1949) The genetical structure of populations. Annals of Human
Genetics, 15, 323–354.
Wu, J., Wang, Y., Xu, J., Korban, S.S., Fei, Z., Tao, S. et al. (2018) Diversifi-
cation and independent domestication of Asian and European pears.
Genome Biology, 19, 77. https://doi.org/10.1186/s13059-018-1452-y.
Young, M.D., Wakefifield, M.J., Smyth, G.K. & Oshlack, A.J.G.B. (2010)
Gene ontology analysis for RNA-seq: Accounting for selection bias. Gen-
ome Biology, 11, R14. https://doi.org/10.1186/gb-2010-11-2-r14.
Yu, Y., Fu, J. & Xu, Y. (2018) Genome re-sequencing reveals the evolution-
ary history of peach fruit edibility. Nature Communications, 9, 5404.
https://doi.org/10.1038/s41467-018-07744-3.
Zhang, H., Peng, S., Cai, L. & Fang, D. (1990) The germplasm resource of
the genus Eriobotrya with special reference of the origin of E. japonica
Lind. Acta Horticulturae Sinica, 17, 6–13.
Zhang, H.Z. & Zhang, Y.D. (1982) A study on native loquat in Hubei pro-
vince. Journal Huazhong Agricultural College, 1982, 86–93.
Zhang, Q., Zhang, H., Sun, L., Fan, G. & Ye, M. (2018) The genetic architec-
ture of floral traits in the woody plant Prunus mume. Nature Communi-
cations, 9, 1702. https://doi.org/10.1038/s41467-018-04093-z.
Zhou, Y., Massonnet, M., Sanjak, J.S., Cantu, D. & Gaut, B.S. (2018) Evolu-
tionary genomics of grape (Vitis vinifera ssp. vinifera) domestication.
Proceedings of the National Academy Sciences of the United States of
America, 114, 11715–11720. https://doi.org/10.1073/pnas.1709257114.
Zhou, Z.K., Jiang, Y., Wang, Z., Gou, Z., Lyu, J., Li, W. et al. (2015) Rese-
quencing 302 wild and cultivated accessions identifies genes related to
domestication and improvement in soybean. Nature Biotechnology, 33,
408–416. https://doi.org/10.1038/nbt.3096.
Zhu, G., Wang, S., Huang, Z., Zhang, S., Liao, Q., Zhang, C. et al. (2018)
Rewiring of the fruit metabolome in tomato breeding. Cell, 172, 249–261.
https://doi.org/10.1016/j.cell.2017.12.019.