Assuring food security to indomitable population surge in view of ghastly exhausting natural resources including land, labor, energy and above all looming large climate change has become a global concern. Consequent upon environmental pollution and curtailed input response, the production of high-quality food must increase with application of inputs. Thus, task of breeders is very onerous to focus on the quantitative agronomic traits that have the potential to increase yield so as to ensure food and nutritional security to burgeoning surge of global population. Pigeonpea is majorly used as dal and it is important component of diet as they comprise good source of protein that complement well with cereals
Varshney et al., (2010) and
Varshney et al., (2012). Its ability to survive and produce high protein food even under stress conditions helps in providing food and nutrition security to subsistence farmers and therefore, it may be considered as the ideal rain fed legume crop of small-holder farmers. Recently, world first grain legume hybrid of pigeonpea ICPH 2671 was released for the commercial cultivation in India and it showed 47% yield advantage over the check variety “
Maruti” in multi-location testing of 4 years. Unfortunately, to develop such kind of hybrids, breeder used to make thousands of random crosses between cytoplasmic male sterile (CMS) lines and tester lines and hence development of hybrids is a cumbersome process. In such case heterosis breeding has demonstrated a remarkable success story for qualitative and quantitative enhancements of grain production.
In the current era of crop improvement in complementation with emerging science of genomics, it has become amply possible to predict phenotype from the genotype
Varshney et al., (2009) and
Patel et al., (2010). The cutting edge large scale DNA sequencing and molecular markers have led to measuring genome wide genetic similarity and dissimilarity in plant species and populations
Varshney et al., (2017). Molecular markers have been used for studying genetic diversity for the examination of genotype frequencies for deviations at individual loci and characterization of molecular variation within or between populations
Varshney et al., (2012). Markers based genetic diversity along with the phenotyping data have been widely used for predicting best possible heterotic combinations. In addition to this, heterotic groups identified via genetic diversity analysis are validated through multi-location evaluation of intra-pool and inter-pool crosses, this validates the optimum genetic distance among parental material for attempting maximum pigeonpea hybrid vigor. In this review, we summarize the status of genomic approach for defining heterotic pools in pigeonpea.
Overview of pigeonpea hybrid breeding technology
The first hybrid was reported in maize (Zea mays) and foresaw the potential of this phenomenon in enhancing crop yields
(Shull, 1908). Additionally, plant breeders of cross pollinated crops designed suitable mating and selection schemes to enhance yields by exploiting hybrid vigour. However, in several other case dominant genes in generally contribute for hybrid vigour, it was considered useful for cross pollinated crops; but later its utility was established in self pollinated crops
Saxena et al., (2013) and
Saxena et al., 2018), they reviewed the phenomenon of heterosis in food legumes and concluded that dominance, over dominance, additive and various inter allelic interactions play a significant role in the expression of hybrid vigour. They further postulated that the likelihood of obtaining heterotic crosses in pigeonpea is high because this crop also has a fairly good inherent capacity to carry a considerable genetic load of recessive genes due to partial natural out crossing in the crop. In several of the following review,
Varshney et al., (2010) showed that in pigeonpea consisting of several of the important economic traits such as seed yield, pods/plant, plant height, seed size and also in several other case seeds/pod are mainly controlled by both additive as well as non additive genetic variances, in addition to this, the level of realized heterosis for seed yield in pigeonpea is comparable to other crops in which commercial hybrids have already made a mark in global agriculture. Also various report in which mentions that male sterility in pigeonpea germplasm led to the selection of genetic male sterility systems that was controlled by single recessive gene
Saxena et al., (2013). In fact, various plant breeding programmes was launched to generate valuable data on the extent of hybrid vigour and various other plant specific related issues for large scale hybrid seed production in pigeonpea. Moreover, GMS hybrids showed 25-30% heterosis for seed yield in farmers’ fields with wide adaptation, but various seed production difficulties and seed quality concerns did not permit commercialization of these hybrids
(Saxena et al., 2013 and
Saxena et al., 2015). The hybrid breeding programme at ICRISAT was then shifted towards developing a more efficient cytoplasmic-nuclear male-sterility (CMS) system.
Selection of parental lines
The parents we selected were based on a study investigating genetic diversity of ICRISAT-bred hybrid pigeonpea parents and are considered to be a fair representation of the original parent population as they maintained the same cluster structure and similar allelic variation as those in the original population. Historically, the majority of ICRISAT B- and R-lines developed at earlier stages were derived directly from inbred breeding programs with many common ancestors shared and selected under the same environment with similar agronomic criteria without further breeding, which resulted in a relatively high genetic uniformity among hybrid pigeonpea parents
(Varshney et al., 2010). This could be one of the reasons for the lower hybrid pigeonpea heterosis observed in the semi-arids environment
(Tikka et al., 1997). In the last a few years, this issue has been addressed by separating the hybrid breeding from inbred breeding programs and by developing B- and R-line heterotic groups individually to maximize genetic diversity among hybrid pigeonpea parents
(Reif et al., 2003a).
Improvement of pigeonpea parental lines
The breeding lines require the development of elite parental lines either the three-lines or two- lines system. The three-line hybrid system consist cytoplasmic male sterile line (CMS), maintainer line and restorer line, while the two- lines system include CMS and restorer line. However, an alternative way of exploiting hybrid is to use of the thermo-sensitive genetic male sterile lines (TGMS) as female parents, for the developing two-line hybrids
(Pazhamala et al., 2015). The development of the superior parental line in terms of disease resistance and grain production has major advantage. Such, type of the parental lines are the prerequisite for the efficient hybrid breeding programme. The use of molecular marker technology has been shown effective in tracking and introducing genes from the resistant donor parents to susceptible parents Table 1, which has significant application for parental lines improvement. In addition to this, various trait mapping for hybrid breeding programmes including fertility restoration, TGMS, wide compatibility, male sterility has major advantage in parental lines improvement Table 2.
Heterotic groups based on markers
Genetic diversity estimates are helpful in classifying germplasm into heterotic groups for hybrid crop breeding. Earlier, the relative performance of inbred lines of known origin and pedigree was commonly used, which largely relies on breeders’ empirical experience, to combine parents from different genetic backgrounds to develop heterotic hybrids. Molecular markers have been used in pigeonpea to assess the genetic relationships of pigeonpea ecotypes or sub-species
(Varshney et al., 2012) and hybrid pigeonpea parents
(Varshney et al., 2017; Patel et al., 2020 and Shekh
et al. (2015). However, information is scarce on assessing heterotic groups among semiarid pigeonpea inbred lines and populations and no conclusive study has been conducted to clearly defined heterotic groups of semiarid hybrid pigeonpea parents. Many of those studies investigating genetic diversity in pigeonpea with molecular markers were dealing with large pools of sub-species or ecotypes, such as ICPL 87119, Asha, Maruti from pigeonpea germplasm collections, but with limited value to practical hybrid pigeonpea breeding due to the inability to produce yield heterosis. For example, mass vegetative growth and partial fertility in hybrids between sub-species. Heterotic groups that are applied in breeding and production are different from the parental groups generated from germplasm collections based on molecular markers Table 3. It is still a challenge to find agreement between high, producible yield heterosis and high divergence among pigeonpea sub-species or ecotypes.
Combining ability and heterotic group
It is well known that inbred lines are homogeneous and homozygous in nature. Such, inbred lines when crossed lead to hybrid vigor depending upon appropriate gene action. They differ in combining ability that in turn hinges on type of gene action, being additive for general combining ability and dominance and non-allelic interactions for specific combining ability. Thus the favourable combination depends on the type of additive and non-additive gene action that controls quantitative character
(Reif et al., 2003a). The inbred lines that combine well with a series of testers, theses inbred line have a good general combining ability (GCA) and inbred lines that combine well with specific cross that inbred lines has specific combining ability (SCA). The selection of parents from different heterotic groups is cardinal to the success of hybrid breeding programme and in this direction the combining ability of the parents entailing both general and specific combining ability is one of the important tools for determining the next phase of breeding strategies
(Reif et al., 2003a).
The combining ability a priori between two inbred lines is explained by the genetic distance of the parents, their mode of pollination and mid parent heterosis (MPH) values. The traditional plant breeding method is hamstrung by lack on information one genetic relationship of parents, morphological characteristic and geographic origin of parent with their wild relative germplasm for obtaining parents from different heterotic groups with good combining ability (Reif
et al., 2010). Conventional plant breeding based combining ability depend on the test cross performance. Compare to such traditional method, molecular marker based selection of parental line has provided a new way to get a good combination. However, molecular marker based genetic distance and heterotic group used for the selection of the parental lines could not accurately predict parental combination unless DNA based molecular markers was linked to genes affecting a trait. Thus, marker based genetic diversity together with phenotyping data have been used for predicting heterosis and developing heterotic group.
Genetic distance and heterosis
Genetic distance used for the measure the genetic difference between different plant species within population. Such, population have many similar genes with small genetic distance. It indicates that they are closely related and have a recent common ancestor
(Reif et al., 2013). The genetic distance is useful for the reconstructing the history of the common populations and understanding the origin of biodiversity
(Xie et al., 2014). For example, the genetic distance between different inbreeds are often investigated in order to determine which breeds should be protected to maintain genetic diversity.
High degree of the heterozygosity in the genome at the homologous chromosomes is responsible for heterosis
(Bansal et al., 2012). The heterozygosity can be increased by the crossing genetically distinct parental materials,
i.
e. materials belonging to genetically divergent parents
Reif et al., (2003b). Such, genetically distinct parental combination have great interest for the breeders. However, identifying specific gene located at a specific place is one of important task in plant breeding. The allelic variations at these loci cause phenotypic variations between different plant species
(Riedelsheimer et al., 2012). The random fluctuation of allele frequencies also produces genetic difference between different populations, this process is known as genetic drift., In addition to this polymorphic markers measure genetic diversity between closely related inbreeds lines. Moreover, SSR and SNPs basis QTL mapping have high applicability to identify diverse parental line from the evolution rate, this evolution rate particularly useful for working out relationships among closely related parental lines for the next generation hybrid breeding programmes.
The development of heterotic pigeonpea hybrid using genomic which include different types of molecular markers; next generation sequencing (NGS) based genotyping widely apply for the selection of the diverse parents. The construction of heterotic pool from the different cytoplasmic male sterile line (CMS), maintainer line, restorer lines are applied for efficient hybrid breeding programme
(Reif et al., 2010) and it will change the future breeding strategies. The trait mapping approach which include fertility restoration, temperature sensitive genetic male sterility (TGMS), wide compatibility and combining ability are widely apply for the hybrid breeding programme. Although, genomic selection using best linear unbiased prediction (BLUP) and genomic estimated breeding values applies for the selection of superior lines and these all strategies for heterotic hybrid combination are described in Fig 1 and 2.
