Mapping Populations for the discovery of Gene(s) and QTLs in Crop Plants
Authors: Kiran B. Gaikwad1 and Sushma Rani2
1Scientist, Division of Genetics, ICAR- Indian Agricultural Research Institute,
New Delhi - 110012, INDIA
2Senior Research Fellow, Division of Genetics, ICAR- Indian Agricultural Research Institute, New Delhi - 110012, INDIA

A population used for mapping of the gene(s) or quantitative trait loci (QTLs) is commonly known as a mapping population. A suitable mapping population, an ideal molecular marker system and user-friendly software for the analysis of genotypic and phenotypic data is a prerequisite for the for mapping of genes or QTLs. Mapping population consists of individual plant progenies that are originated from the hybridization between two contrasting parents of one species or related species. The parents must be diverse, both at phenotypic as well as genotypic level and particularly for the trait of interest. It is considered as chief genetic tools in linkage map construction since they are used to identify genetic loci that influence the expression of phenotypes and to determine the recombination distance between loci.

Criteria for the development of mapping populations:

  • Selection of parents for developing mapping population: Selection of parents for establishing mapping population is immensely crucial for the identification of genetic loci associated with the trait of interest and in successful map construction. Following points d taken in account/ considered while selection of parents
  • The parents should be completely homozygous.
  • In those crop species where doubled haploids (DHs) development is successful, selection of DH parents would be beneficial as the residual effect of heterozygosity will be eliminated.
  • The parents must be genetically diverse for an array of quantitative traits and also show a high level of molecular marker polymorphism for the construction of marker rich genetic map.
  • Preferably, the parents should belong to same species. Use of unadapted or crop’s wild relatives in developing mapping population will encounter issues of non-complete chromosomal pairing, low recombination rate, preferential gamete transmission to the progeny etc.
  • Size of mapping population: Mapping population should be as large as possible if resources permit. With respect to QTL mapping, large mapping population provides the advantage of identifying more number of QTLs for the traits of interest. Similarly, it will also reduce the confidence interval in linkage mapping. The number of individuals in a mapping population depends on the objective of the mapping studies. For fine mapping or positional cloning of genes, population of more than thousands individuals must be exploited / employed. Ideally, for QTL mapping studies, the population of more than 500 individuals is generally sufficient.

    Choice of mapping population:

    For preliminary mapping studies, mapping populations like F2, F2:3 and Bulk Segregants Analysis (BSA) could serve as good candidates. Long-term mapping populations viz., RILs, NILs, CSSL and Introgression lines population etc. can be used for phenotyping of trait of interest authentically.

    Types of mapping populations:

    Different types of mapping populations that are often used for study are : (1) F2 population; (2) F2 derived F3 (F2:F3) populations; (3) Backcrosses; (4) Doubled haploids (DHs); (5) Recombinant Inbred Lines (RILs); and (6) Near-isogenic Lines (NILs) (7) Immortalized F2 population (8) Chromosomal Segment Substitution Lines (CSSLs), (9) Backcross Inbred lines (10) Advanced Intercross Lines (11) Recurrent Selection Backcross Population (RSBP) (12) Multi-parent Advanced Generation Intercross Population (MAGIC) (13) Nested Association Mapping Population (NAM).
F2 population:

  • Produced by selfing or sib mating F1 individuals from a cross between selected parents.
  • F2 individuals are products of single meiotic cycle
  • Ratio expected for dominant marker is 3:1 and for codominant marker is 1:2:1
Advantages
  • Best population for preliminary mapping and genes with major effect.
  • Requires less time for development.
  • Provide an estimate of additive, dominance and epistatic components of the genetic variance.
  • Ideal for the identification of Heterotic Loci or hQTLs as they provide estimates of dominance, overdominance or pseudo-overdominance and epistatic components of gene action.
  • In clonally propagated crops F2 plants can be multiplied and maintained as clones.
Disadvantages
  • F2 populations are of limited use for fine mapping and mapping of QTLs.
  • F2 populations cannot be replicated in seed propagating crops; therefore quantitative traits cannot be effectively mapped.
  • Due to only one cycle of recombination, maker identified to be linked with the gene of interest are likely to be located at a longer distance from the gene.
F2 derived F3 (F2:3) population:
  • Obtained by selfing of the F2 individuals for a single generation.
  • This mapping population is not perpetual as F2 population.
  • Suitable for mapping oligogenic traits controlled by recessive genes and QTLs.
Advantages
  • Suitable for mapping oligogenic traits controlled by recessive genes and QTLs.
  • Easy to construct
Disadvantages
  • This population is not perpetual or immortal.
  • Require an extra season for the development than F2 population.
  • In F3 generation, F3families are segregating for majority of the loci hence, cannot be replicated.
  • Estimates of dominance, overdominance and epistatic components of gene action are underestimated due to inbreeding.

    Backcross Mapping Population:
  • Backcross populations are generated by crossing the F 1 ­with either of the parents. When F1 is crossed with a dominant parent it is denoted by B1 and when crossed with a recessive parent it is denoted by B 2.
  • For genetic analysis, F1 is backcross with a recessive parent.
  • When the co-dominant marker is used in BC population, the order of backcross (F1 is crossed with either B1 or B 2) and phase of linkage (either coupling or repulsion) do not matter; Co-dominant marker will always give 1:1 segregation ratio.
Advantages
  • Backcross population can further be utilized in Marker Assisted Backcross Breeding.
Disadvantages
  • This population is not perpetual.
  • They cannot be evaluated in replicated trials hence mapping of QTLs is not feasible.
  • Construction of BC population requires additional efforts of crossing F1 with either of parents.
  • Require an extra season for the development than F2 population

    Doubled Haploids (DHs):
  • DH plants are developed from chromosome doubling of haploid plants generated from anther/pollen grains of F1 plants. They can be made from interspecific crosses by the preferential elimination of chromosomes from one of the parents.
  • DHs are also products of one meiotic cycle.
  • DH population is completely homozygous at all the loci in the genome with no residual heterozygosity.
  • The expected ratio of the marker is 1:1, irrespective of genetic nature of marker (whether dominant or codominant).
Advantages
  • DH population is perpetual.
  • It can be replicated over locations and time, making it suitable for mapping of oligogenic and QTLs.
  • Homozygosity can be achieved very quickly; therefore it can be used in breeding programmes for varietal development.
Disadvantages
  • More technical skill, resources are required for the production of DH lines at very large scale.
  • Genotypes show variable response for DH production protocol.
  • Many crop species do not have DH production protocol.
  • Treatment with colchicine induces genetic variation in the population.
  • Only additive x additive component of genetic variance could be worked out as DH lines are completely homozygous.
  • DH population is not suitable for mapping heterotic loci or hQTLs.


Recombinant Inbred Lines (RILs):

  • RILs consist of homozygous lines produced by selfing of individual F2 plants till they attain complete Homozygosity.
  • Preferably, RILs are developed by Single Seed Descent (SSD) method for more than 6 generations.
  • During the development of RILs selfing is preferred over sib mating because, the rate of reducing heterozygosity in selfing is half (50%) than that of the previous generation; in sib-mating, it’s one-fourth. Population developed by ib mating required twice many generations than selfing to attend the same level of Homozygosity.
  • Pedigree or Bulk method of breeding can be employed in the development of RILs
  • RIL population consist of only two types of individuals i.e. two homozygotes (AA or aa); therefore the segregation ratio for both dominant and co-dominant marker is 1:1.
Advantages
  • RILs are perpetual
  • They can be replicated over locations and time; therefore RIL S are very important for QTL mapping.
  • RILs enable the identification of tightly linked markers due to many recombination events.
  • RILs can be used for the estimation of additive and additive x additive component of genetic variation because of complete homozygosity.

Disadvantages

  • Development of RILs required considerable time.
  • RIL could become genetically variable due to natural outcrossing, mechanical mixture etc.; therefore their maintenance and storage required care.
  • In crops with high inbreeding depression have difficulty in development of RILs.
Near-Isogenic Lines (NILs):

  • NILs are developed by backcrossing. Donor parent (DP) is crossed with recurrent parent (RP) to create F1. This F 1 is backcrossed to recurrent parent for 4-5 generations depending on the complete recovery of RP genome.
  • NILs are identical in genetic constitution to their RP except for the gene of the interest transferred from the DP.
  • In each backcross (BC) generation stringent selection is practiced for the gene or trait being introgressed from DP; as with every generation of BC, the proportion of DP genome is reduced by half.
  • Similarly, with every generation of BC, the chances of elimination linked DP genome with the gene of interest get an increase due to recombination.
  • The segregation ration is 1:1 for both dominant and co-dominant markers due to Homozygosity of individuals.
Advantages
  • NILs are perpetual.
  • NILs are useful in fine mapping of genes and positional cloning of QTLs.
  • NILs can accurately estimate the effect of QTL or gene contributed by donor parent (DP). Because, the complement chromosome complement except for the DP segment is contributed by the recurrent parent (RP), therefore the epistatic effect is eliminated.
Disadvantages
  • Required 5-6 backcrosses for the development of RILs.
  • The gene / QTL introgressed from DP can only be tagged.
  • When NILs are developed by employing wild or unadapted germplasm, the problem of linkage drag, preferential transmission of gametes from DP is involved.
Immortalized F2 Population:
  • The IF2 population is developed by selecting individuals from RILs e.g. AAbb x aaBB and crossed to produce four types of individuals viz., AABB, AAbb, aaBB, and aabb. These individuals are crossed in the following fashion to produce six heterozygous genotypes.
Six possible RIL combinations Six heterozygous genotypes
AABB X AAbb X aaBB X aabb AABb AaBB AaBb
AAbb X aaBB X aabb AaBb Aabb
aaBB X aabb aaBb
  • In IF2 population, all the genotypes are represented as they are represented in F2.
  • It combines the advantage of the segregating F2 and the eternal RIL population
Advantages
  • The IF2 population can be evaluated in replications over locations.
  • It can allow the identification of heterotic loci or hQTLs and QTLs for agronomically important traits.
  • Estimates of additive x dominance and dominance x dominance effects can be worked out.
Disadvantages
  • Construction of IF2 requires large no of crosses with a good amount of seed for replicated trials. It would become difficult in self-pollinating crops where crosses are are generated through hand pollination.
Chromosomal Segments Substitution Lines (CSSL):

  • They are also known as introgression or inter-varietal substitution lines.
  • CSSL are homozygous lines each having a different segment from donor parent (DP) in the genetic background of the recurrent parent (RP). Complete DP haploid genome complement is represented in CSSL.
  • When wild or unadapted germplasm is employed in the development of CSSL is known as alien introgression lines and when DP is another cultivated variety of same species is known as inter-varietal substitution lines.
  • CSSL is developed by backcrossing F1 with DP for 5-6 generations followed by selfing for two or more generations to develop lines which are homozygous for the introgressed segment.
Advantages
  • CSSL is perpetual.
  • CSSL is suitable for mapping major genes and QTLs.
  • CSSL and RP differ only for the introgressed segment from DP, therefore, any difference between RP and CSSL are directly attributed to the introgressed donor segment. Hence, the effect of introgressed gene / QTL is accurately estimated.
  • CSSL is free from epistatic effect as almost entire genome is similar to RP genome.
  • CSSL serves an excellent tool for mapping Heterotic QTLs.
  • CSSL can be evaluated over time and space. Therefore identifying QTLs with major and minor effects is feasible.
  • CSSL can be used for fine mapping of gene and cloning of QTLs.
  • CSSL can be used as advanced breeding lines for the development of variety.
Disadvantages
  • If wild or unadapted germplasm is used as DP then problem of linkage drag, sterility in the lines, preferential transmission of gametes from DP origin persist.
  • Backcross Inbred Lines (BILs) BILs are developed by crossing F1 to one of its parents and continue selfing of BC1F1 progenies to obtain homozygous lines.
  • The parent which exist a high value for the trait of interest is used for backcrossing.
Advantages
  • One backcross followed by continuous selfing may yield transgressive segregants.
Advanced Intercross Lines (AILs):

  • AILs are developed by intermating of selected individual plants of F2 or subsequent generation.
  • Intermating of individuals among the segregating generations maintain the heterozygosity in the population and allow crossing over between QTL and linked marker. This will lead to the identification of closely linked markers to the QTL.
Advantages
  • AILs are good for QTL mapping studies.
Recurrent Selection Backcross Population (RSBP):

  • In RSBP, parents with high trait value (from DP) and low trait value (from RP) are crossed to produce F1. This F1 is backcrossed to RP to generate BC1F 1. Further few backcrosses are made with RP.
  • In each backcross, individuals with high phenotypic value are selected and backcrossing was done with RP to develop RSBP.
  • The trait of interest will be in heterozygous condition during recurrent backcrossing whereas other traits which do not have selection pressure will become rapidly homozygous.
Advantages QTLs with major effect can only be mapped.

Disadvantages
  • Several QTLs with minor effect will be lost as only QTLs with higher phenotypic value will be selected in the recurrent backcrossing.
Multi-parent Advanced Generation Intercross Population (MAGIC):

  • The MAGIC population is RILs produced from a complex cross involving several parental lines (usually 8).
  • Parental lines employed in developing MAGIC population are of diverse origin with diverse phenotypic traits
  • Eight parental lines are crossed in pairs to form 4 single crosses; these 4 single crosses are then crossed in pairs to generate 2 double crosses; these 2 double crosses are then crossed to produce eight parental complex cross. This cross is further carried forward by SSD to generate RILs which constitute a MAGIC population.
Advantages
  • MAGIC population is perpetual.
  • This population is mainly used for association mapping studies and also used for linkage mapping.
  • This population serves as valuable breeding material for the development of variety. The mega varieties of Wheat and Rice are the perfect examples/output of MAGIC population.
  • Due to the complex pedigree structure, MAGIC population offers great potential for dissecting genomic structure and improving breeding population.
Disadvantages
  • Development of MAGIC population requires ample of resources.
Nested Association Mapping Population (NAM):

  • NAM population involves founder parents which are selected based on their diverse source of origin and contribution of different traits. The idea is to represent maximum diversity in the founder lines.
  • NAM population is developed by crossing diverse founder parents with a common parent.
  • Each founder parent is crossed to common parent and set of RILs (250-300) from each cross is developed using SSD method.
Advantages
  • NAM is used in genome-wide association studies
  • Identification and dissection of QTLs of complex traits and correlate the QTLs to homologs and candidate genes.
Disadvantages
  • Development of NAM population is difficult task
  • Handling of RILs from many crosses needs resources.
Conclusion:

In order to discover gene(s) or QTLs associated with trait of interest, it is essential to establish proper genetic populations, select appropriate DNA markers and construct genetic maps. The developmental procedures of different mapping populations are well explained in this article and will certainly benefit the researchers. It is stated that, “traditional breeding often depends on experience, while molecular breeding relies on genetic mapping population.” Therefore, this article chapter reviewed all most all the mapping populations very precisely with their procedure to develop and its merits and demerits as well.

References:


1. Singh BD and Singh AK (2015) Marker-Assisted Plant Breeding: Principles and Practices. Springer. DOI: 10.1007/978-81-322-2316-0

2. Tian J, Deng Z, Zhang K, Yu H, Jiang X, Li C. (2015) Genetic Analysis Methods of Quantitative Traits in Wheat. In: Genetic Analyses of Wheat and Molecular Marker-Assisted Breeding, Volume 1. Springer, Dordrecht


About Author / Additional Info:
I am working as Scientist at Division of Genetics, Indian Agricultural Research Institute, New Delhi.