Mapping Populations

RILs, NILs
• Population used for mapping the genes is commonly called as mapping
population and they usually obtained from controlled crosses.

Fig: Pictorial representation of development of mapping population

Recombinant Inbreed Lines (RILs)
• Also called F2 derived lines
• RILs are homozygous line derived from individual F2 plants from suitable
cross.
• RILs are created by single seed descent selection from F2 plants through at
least five or more generations of continued selfing.
• Seeds harvested separately at end of SSD to obtain as many RILs as there are
individual plants.
Advantage of RILs
• They can be maintained
• They provide maximum information for dominant marker
• Ideal for QTL mapping
• RILs allow construction of molecular map with concerned gene

Disadvantage
 Require long time (6-8 yrs) to develop RILs
Near-isogenic Lines (NILs)
 Near-isogenic lines (NILs) are strains which genetic makeups are identical
except for few specific locations or genetic loci.
• The first strategy used for molecular mapping was based on NILs.
• NILs can be developed by repeated selfing or backcrossing of F1 with
recurrent parent.
• Near isogenic lines are frequently the product of plant breeding
programs, where the objective has been the introgression of a desirable
character or trait (gene) from a donor parent into an otherwise
agronomically acceptable cultivar (recurrent parent).
Merits
• Used for fine mapping
• Like DHs and RILs, NILs are also Immortal population
• Suitable population for tagging the trait, wherever such population is
available
• NILs are quite useful in functional genomics

Demerits:
• Many generations required to develop NILs
• Increased cost, time and efforts
• Used in molecular tagging of concerned gene, but not for linkage
mapping
ISOGENIC LINES
• usually refer to two lines have exact same genetic makeup, with one
gene in difference.
• Researchers refer the 'wild type (non-transgenic)' line and the transgenic
line derived from this wild type line as isogenic lines.
• They basically have only 1 gene different
• Vegetatively propagated clones are isogenic and lines of inbreeders
become isogenic after repeated self-fertilization.
Crop Improvement
• Crop improvement refers to genetic alteration of plants to satisfy human
needs.
• The selection of naturally occurring variants is the basis of crop improvement.
• Through a long history of trial and error, a relatively few plant species have
become the main stay of agriculture and thus the world's food supply.
• The selection process was unconscious in many cases.
• For example, in wild wheats, the grains scatter by separation of the seed from
the seed head. When these grains were harvested by cutting the heads with a
sickle, an unconscious selection occurred for "non-shattering" types that
would then be continually replanted.
• The process of domestication identify useful wild species combined with a
process of selection, hybridization and genetic recombination that brought
about changes in appearance, quality, and productivity.
Rice Improvement
Origin and genetics
• Oryza sativa L., the principal cultivated species of rice
• Based on archeological evidence, first domesticated in the region of the Yangtze
River valley in China nearly 10,000 years ago including north eastern India,
bangladesh, Burma, Thailand, Vietnam.
• The genus Oryza belongs to the family Poaceae and sub family oryzoideae.
• Oryza have two cultivated species. These two species are Oryza sativa (Asian rice)
and Oryza glaberrima (African rice) known for commercial purpose among
twenty- three species of rice.
• Oryza glaberrima cultivate in limited area of south Africa.
• Oryza sativa is differentiated into three sub species, indica, japonica and javanica
based on their commercial production zones.
• Rice is a true diploid (2n=24) with twelve chromosome pairs.
• O. sativa (2n=2x=24) has AA genome formula. O. glaberrima (2n=2x=24) does not
pair with Oryza sativa and has AgAg genome formula.
• It meets more than 50% of the total calorie requirement of the Nepalese
people
• It is cultivated in a wide range of agro-climatic regions of Nepal under varying
topography, climates and altitudes.
• The crop is grown in Nepal ranging from 60 to 3050 MASL, the highest rice
cultivation point in the world.
• Out of total cultivated land of paddy, majority of the area falls in Terai and
Inner Terai regions and rest falls in hills, mid hills and other parts of the
country.
• This crop is grown in irrigated as well as rain-fed condition.
• This crop is grown mainly in two seasons; rainy and spring seasons.
• In rainy season, it is grown in upland as well as low land while in spring season
in low land where irrigation facility is available.
Breeding objectives
• Higher grain yield and straw yield
• Stability of the production
• Higher harvest index (Harvest index (%) = Grain yield / Biological yield × 100)
• Lodging and shattering resistance
• High tillers / unit area
• Resistance to insects/pest and diseases
• Wider adaptability
• Tolerance to stresses
• Higher panicle length and more number of grains/panicle
• Earlier maturity
• Erect leaf characters
• Dwarf plant height
Varieties
A. Spring Season:
 Chaite 2, Chaite 4, Mallika, Bindeswary, Laxmi, Chaite, Chandina, IR 24,
Parwanipur 1, CH 45.

B. Main Season:
 Chandan Nath 1, Chandan Nath 3, Manjusree 2, Khumal 11, mansuli,
Khumal 6, Machhapuchhre 3, Radha 11, Radha 12, Radha 4, Radha 7,
Radhakrishna 9, Chhomrong local, Khumal 9, Khumal 7, Khumal 5, Palung
2, Ghaiya 2, Khajura 2, Barkhe 2, Makawanpur 1, Khumal 2, Khumal 4
Method of Breeding
1. Introductions
2. Pureline selection
3. Mass selection
4. Hybridisation followed by selection: backcross breeding, pedigree selection.
5. Genetic engineering
6. Tissue culture
7. somaclonal variation
Research Activities:
• Rice research was started in 1951 in Nepal
• A total of 930 local varieties from 54 districts were collected and intensive
evaluation was carried out at Parwanipur and Khumaltar.
• Initially, exotic rice variety from Taiwan were introduced, evaluated and
were found to high yielding in kathmandu valley.
• Introduction and evaluation of indica rice lines were carried out since 1959
at parwanipur agriculture station.
• After testing of various exotic materials, CH 45 was recommended as the
first modern variety in Nepal.
• To carry out the efficient and qualitative research in rice, National Rice
Improvement Program was established in 1972.
Since then, following research activities are being carried out in Nepal.
1. Germplasm collection and evaluation of local landraces
2. Germplasm introduction
3. Breeding works: Resistance to diseases, yield, adaptation, height,
aroma and taste, maturity.
4. Pathological researches mainly on blast, bacterial blight, brown spot,
sheath blight, foot rot, sheath brown rot and others.
5. Entomological researches mainly on stem borers, brown plant hoppers,
green leaf hoppers, gall midge, Rice hispa, Leaf roller, Seed bed beetle.
Likewise researches on predators of leaf and plant hoppers.
6. Agronomical and physiological researches
Seedling age, seeding date, seed rate, spacing, weed management,
days to anthesis, days to maturity, number of effective tillers per unit
area, etc.
7. Soil management
Time and dose of fertilisers and manures application
8. Water management:
stage of crop to irrigate the field, number of irrigation.
9. Research on quality aspect:
milling percent, protein content, aroma, cooking quality, etc.
10. Seed production activities:
mainly breeder and foundation seeds.
WHEAT Improvement
• Wheat is the first major cereal crop in the world.
• It stands 3rd position in Nepal after rice and maize.
• But it ranks 2nd major crop in the Terai areas of Nepal.
• Terai region represents about 56% of total wheat cultivated area and
contributes more than 63% of total wheat production in the country.
Origin
♦ Centres of origin are Mediterranean (bread wheat), and Ethiopian
(durums).
♦ He species of Triticum are classified into three ploidy levels; diploid
(2n=2x=14), tetraploid (2n=4x=28) and hexaploid (2n=6x=42).
♦ The hexaploid bread wheat contain three different sets of genome AA, BB,
DD.
♦ Diploid species might have originated from the same common parent
species, which are now differentiated into several genomes.
♦ Evidences indicate that tetraploid species T. turgidum (AABB), the
cultivated emmer and durum wheat evolved from an alloploid T.
monococcum (AA) and an unknown and possibly extinct species containing
BB genomes.
♦ Bread wheat T. aestivum (AABBDD) originated as an alloploid combining T.
turgidum and the diploid species T. tauschi (DD).
Classes of wheat
1. Hard red winter
2. Hard red spring
3. Soft red winter
4. White winter
5. Durum and red Durum
6. Soft red spring

Varieties
Lerma 52, LR 64, Pitic 62, S 331, RR 21, NL 30, HD 1982, UP 262, Lumbini,
Triveni, Siddhartha, Vinayak, Vaskar, Nepal 297, Nepal 251, Annapurna 1,
Annapurna 2, Annapurna 3, BL 1022, Bhrikuti, Annapurna 4, BL 1135, Achyut,
Rohini, Pasang Lhamu, Kanti, Bl 1473
Breeding objectives
1. High grain yield and stability of yield
2. Earlier maturity
3. Lodging and shattering resistance
4. Medium tall plants
5. More productive tillers per unit area
6. Long compact spikes
7. High number of grains per spike
8. Resistance to diseases and pests
9. Drought tolerance
10. Fertiliser responsive
11. High protein content
12. Milling and baking quality
Methods of Wheat breeding
1. Introductions
2. Germplasm collection and Evaluation
3. Pureline selection
4. Mass selection
5. Hybridisation followed by selection: backcross, pedigree method.
6. Genetic engineering
7. Tissue culture
8. Somaclonal variation
Research Activities
• During mid 1960s the yield potential of dwarf high yielding varieties
initiated a scope for raising wheat production in the country.
• Several exotic varieties were obtained through CIMMYT and USAID and
tested under Nepalese environments.
• To organise the research and development works on wheat as a
commodity crop, the National Wheat Development Program was
established in 1972.
• Then in 1990, National Wheat Research Program existed under the Nepal
Agriculture Research Council.
The following research activities are being carried out in Nepal since mid
1960s.
• Germplasm collection and evaluation of local landraces
• Germplasm introduction
• Breeding works: Resistance to diseases, yield, adaptation, height,
maturity.
• Pathological researches mainly on rust, leaf blight, powdery mildew,
loose smut and common bunt.
• Entomological researches on stored grain pests and field insects.
• Agronomical and physiological researches
• Seeding date, seed rate, surface seeding, spacing, weed management,
days to anthesis, days to maturity, sterility and etc.
• Soil management
Time and dose of fertilisers and manures application
• Water management: stage of crop to irrigate the field, number of
irrigation.
• Research on quality aspect: milling percent, protein content, baking
quality, etc.
• Seed production activities: mainly breeder, foundation and certified
seeds.
Plant breeding techniques and methods used in crop
improvement in Nepal
• Breeding technique is the method of reproduction i.e. production of
progeny. It may be either controlled pollination (selective mating) or open
pollinated (random mating).
• Plant breeding methods can be grouped into three categories.
• First is conventional or classical plant breeding methods, which were
developed during the early plant breeding era and are commonly
practiced in most of the breeding institutes. These methods are dominant
in Nepal.
• For self-pollinated crops, classical methods are introduction (primary and
secondary), mutation breeding, landrace enhancement, maintenance
breeding, back crossing, mass selection, pure line selection, bulk method,
heterosis breeding, cultivars mixture (varietal blend), pedigree method
and single seed descent method.
• Second is participatory plant breeding method, which involves farmers
and plant breeders during selection as well as advancing segregating
generations. These methods mostly conducted in farmer’s field, e.g.
participatory plant breeding (PPB), participatory varietal selection (PVS),
farmer’s field trial (FFT) and landrace enhancement.
• Third category is modern plant breeding methods and generally includes
application of biotechnological tools. Broadly there are three methods
under modern plant breeding, namely
1. Molecular marker technology,
2. Plant tissue culture and
3. Genetic engineering.
• Experiment designs used by plant breeders are RCBD, CRD, augmented
design, alpha lattice, split plot, multi-locations/years trial, un-replicated
trial, rod row design (solid seeded lines).
• Most common statistical tools are stability analysis (AMMI, GGE biplot),
multivariate analysis (cluster, PCA), descriptive statistics (frequency, CV,
mean, SE), test statistics (F-test, t-test, LSD, DMRT), ANOVA, correlation,
regression and genetic parameters. Most common software are GGE Biplot,
Agrobase, R, SAS, Minitab

• For Plant breeding trials and generation handling, followings are the
commonly used breeding trials in Nepal:
 Crossing nursery: Growing of male and female parental lines in glasshouse
or field for hybridization
 Initial evaluation trial (IET): On-station replicated yield trial of newly
developed genotypes including check in one location for testing their
overall performance. Also known as preliminary yield trial (PYT).
 Coordinated varietal trial (CVT): Replicated yield performance trial where
varieties and checks are evaluated on more than one location for testing
their adaptability and stability. It is also called multi-location yield trial
(MYT).
 MINIKIT: A small seed kit of modern cultivars distributed free by the formal
research system to promote the newly released varieties under farmers’
management conditions.
 Participatory varietal selection (PVS): Selection of fixed lines (released or
pre-released or advance lines or landraces) by farmers in collaboration with
breeders in their target environments using their own selection criteria.
 On-farm trial: Trial in farmer’s field either managed and controlled by
farmer or researcher. Generally particular technology or variety is tested in
comparison with local one in farmer’s management practices.
 On-station trial: Trial managed by researchers on-station where most of
the agricultural practices are controlled and suitable environment for
particular varieties are created.
 Diversity kit: Also called seed kit, which includes more than one variety
either released, pipelines or landraces in a pack to distribute to the
farmers. This is particularly targeted to increase diversity along with
making farmers access to new varieties.
 Demonstration plot: Growing newly released varieties including local
landrace in farmer’s field or in area accessible to many farmers with the
objective of showing potential of new varieties to the farmers at their own
location.