Search

Pigeonpea [Cajanus cajan (L.) Millsp.] is a short-day legume species and the late maturing genotypes are more photosensitive than early types. To generate information about the inheritance of photo-sensitivity, this study was conducted under natural and artificially extended (16 h) photo-periods using F1, F2 and BC1F1 generations. Under natural photo-period, F1 hybrids showed partial dominance of earliness; while in F2 , a normal distribution that was skewed towards earliness was observed. In contrast under extended photo-period, the spread of F2 data was wide with discontinuities recorded at day 70, 82 and 103. Chisquare tests, when applied to F2 and BC1F1 data, suggested that three dominant genes (PS3 , PS2 and PS1 ) controlled the expression of photo-sensitivity. These genes were found operating in a hierarchical order with PS2 and PS1 genes failing to express in the presence of PS3 gene. Similarly in the absence of PS3 gene, PS2 expressed but it masked the expression of PS1 . Further, PS1 gene expressed only when both PS3 and PS2 were in recessive homozygous state. Hence, the proposed genetic model for photosensitivity in pigeonpea is PS3 > PS2 > PS1 and photoinsensitive genotype being a triple recessive (ps3ps3ps2 ps2ps1ps1 ). .

Pigeonpea is an important food legume crop of semi-arid tropical regions. Plateauing of pigeonpea yield has been worrying breeders for the past 6–7 decades. Serious breeding efforts made during this period resulted in various high-yielding and disease resistant cultivars. However, the gains in pigeonpea productivity have been modest. The authors, while reviewing this situation, conclude that long generation turnover, complexity of biological traits, low selection response and overreliance upon pedigree breeding present the key bottlenecks for this situation. In this paper, some alternative breeding approaches and technologies are suggested for the genetic enhancement of yield stability and stress response of pigeonpea.

In cytoplasmic genetics male-sterility (CGMS)-based hybrid seed production technology, instability of fertility restoration is one of the prime causes behind instable yield performance of hybrids over the wide range of environments which makes better hybrids adaptive to only a specific environment. Therefore, the present study was conducted to investigate the stability of fertility restoration and yield traits of 10 promising CGMS-based pigeonpea hybrids during 2012–2013 at three different environments of India. The results revealed a significant variability among hybrids for fertility restoration and yield traits over the environments. All the hybrids except ICPH 3494 and ICPH 3491 exhibited high (> 80%) pollen fertility and fully male-fertile plants across the environments indicating complete fertility restoration in these hybrids. Hybrids ICPH 2671, ICPH 2740, ICPH 3933, and ICPH 3461 were stable for pollen fertility, fertility restoration, and for days to maturity except ICPH 3461. Hybrids ICPH 2671, ICPH 2751, and ICPH 3461 were stable for number of pods plant−1, whereas ICPH 2671, ICPH 2740, ICPH 3933, ICPH 3461, and ICPH 3762 were stable for grain yield plant−1 with high mean, unit regression coefficient, and non-significant deviation from the regression line. The varying fertility status of hybrids across the environments indicates that fertility restoration is sensitive to environmental conditions.

Summary Hybrids are extensively used in agriculture to deliver an increase in yield, yet the molecular basis of heterosis is not well understood. Global DNA methylation analysis, transcriptome analysis and small RNA profiling were aimed to understand the epigenetic effect of the changes in gene expression level in the two hybrids and their parental lines. Increased DNA methylation was observed in both the hybrids as compared to their parents. This increased DNA methylation in hybrids showed that majority of the 24‐nt siRNA clusters had higher expression in hybrids than the parents. Transcriptome analysis revealed that various phytohormones (auxin and salicylic acid) responsive hybrid‐MPV DEGs were significantly altered in both the hybrids in comparison to MPV. DEGs associated with plant immunity and growth were overexpressed whereas DEGs associated with basal defence level were repressed. This antagonistic patterns of gene expression might contribute to the greater growth of the hybrids. It was also noticed that some common as well as unique changes in the regulatory pathways were associated with heterotic growth in both the hybrids. Approximately 70% and 67% of down‐regulated hybrid‐MPV DEGs were found to be differentially methylated in ICPH 2671 and ICPH 2740 hybrid, respectively. This reflected the association of epigenetic regulation in altered gene expressions. Our findings also revealed that miRNAs might play important roles in hybrid vigour in both the hybrids by regulating their target genes, especially in controlling plant growth and development, defence and stress response pathways. The above finding provides an insight into the molecular mechanism of pigeonpea heterosis.

Rapid growth in population leads to urbanization resulting in considerable land use, land covers changes, and creates a sequence of environmental and food security problems. Due to speedy urbanization the agricultural lands has been converted into no-agricultural activity such as brick production. Brick kilns required larger areas for brick production and it removes agriculturally productive topsoil rich in clay, soil organic matter content and others important soil nutrient that is viable for agricultural growth. In addition to the removal of fertile top soil, brick kilns making process also emits harmful gases into the atmosphere. This harmful gaseous emission from brick kilns impacts the available natural resources and livelihood nearby it. Its emission results in decreased land and plant productivity, lowered ground water levels, and particularly leads to air pollution. It was found that neighbouring areas of brick kilns has low organic matter content and soil nutrients, and high soil electrical conductivity and low pH. It also changes the chemical and biological characteristics of soil and water. A change in physical, chemical and biological parameters of soil and water leads to reduce cultivated areas, and finally reduces agricultural production and productivity. It also directly impacts the food production system and could threaten the livelihood of present and future generations by degrading agricultural soil and consequently also eroding the economic basis of farmers.

Pigeonpea breeding activities started about a century ago and for decades only late maturing cultivars dominated the global cultivation. Historically, no early maturing cultivar was available for a very long time and breeding of such varieties started in the third quarter of 20th century but at a low key. From these efforts, some pigeonpea varieties maturing in 90–150 days were bred. Information gathered from various sources revealed that the first few early maturing genotypes originated through spontaneous mutations in the late maturing field‐grown landraces. In other cases, transgressive segregation and induced mutations also produced early maturing varieties. At present, the high yielding early maturing cultivars are contributing significantly towards widening the adaption barriers and in the diversification of some age‐old cropping systems. In this paper, the authors, besides discussing the importance of early maturing cultivars in present agricultural systems, also summarize information related to the origin of primary sources of earliness.

Adaptation of pigeonpea [Cajanus cajan (L.) Millspaugh], a short-day species, is restricted due to its sensitivity to photo-period. Earliness in this crop is reported to be linearly associated with photo-insensitivity; and this provides an opportunity to breed widely adapted cultivars through the selection for earliness. This research note reports breeding of the earliest maturing pigeonpea germplasm at ICRISAT. This germplasm, nicknamed as ‘super early’ and bred through the selection of transgressive segregants matured in

Legumes are an integral part of the ecosystem that contributes to sustainable agricultural development across the globe and ensures nutritional security, particularly among the poor segment of the society. Among several legumes cultivated in the world, common bean, chickpea, cowpea, groundnut, lentil, pigeonpea, and soybean are the major seven legumes highly preferred across the globe. The combined production of these major legumes has followed an increasing trend with the global production increase by 548.6% between triennium ending 1961–1963 and 2014–2016 owing to a combined effect of area expansion by 152.6% (128.37 m ha) and productivity enhancement by 85.9% during the same period. The global annual growth rates (AGRs) of total area, production, and yield of these major legumes during the 1961–2016 period are 1.7%, 3.5%, and 1.2%, respectively. The highest AGR for production was observed in the case of soybean (4.5%) followed by cowpea (4.1%), lentil (3.5%), groundnut (2.2%), pigeonpea (1.8%), common bean (1.5%), and chickpea (1.1%), while the highest AGR for productivity was observed in the case of groundnut (1.5%) followed by soybean (1.4%), cowpea (1.4%), lentil (1.4%), common bean (1.1%), chickpea (0.9%), and pigeonpea (0.4%). The global future demand and supply projections of these legumes clearly highlight the importance of developing countries in legume production. The country-wise demand and supply gaps and the changes in pattern of their utilization over time will drive the future research focus on legumes in those countries.

Farming communities, around the world, who earn their livelihoods through their hard work with limited resources and many times under unfriendly and risky agricultural environments are the main providers of plant proteins to masses by cultivating legumes. Besides proteins, legumes also contain valuable vitamins, mineral and fibre necessary for nutritional security. Globally, over a dozen legume species are cultivated in different agro-ecologies and cropping systems, but seven of them, namely, soybean (Glycine max), groundnut (Arachis hypogaea), cowpea (Vigna unguiculata), common bean (Phaseolus vulgaris), chickpea (Cicer arietinum), lentil (Lens culinaris) and pigeonpea (Cajanus cajan), hold promise with respect to their adaptation, productivity, international trade and consumer preferences. Legumes as a group, unfortunately, carry a tag of low productivity, and in spite of reasonable research efforts in general, their yield enhancement goals still remain unfulfilled. For this bottleneck various factors such as lack of high yielding cultivars, low research priority, inadequate inputs, relegation of the crops to second-grade lands, disease and insect losses and use of the age-old research tools and technologies can be held responsible. It seems that legume researchers have already lost valuable time and opportunities to provide farmers with high yielding cultivars with wide adaptation and incurring least damage due to biotic and abiotic stresses. Presently, the adverse effects of climate changes are also looming large, and hence, there is compelling need to re-emphasize the research priorities on a global basis. To highlight the importance of legumes to the human race and to make the legumes (including pulses) affordable to the poor, the 68th session of the UN General Assembly declared 2016 as the “International Year of Pulses”. It seems now the time is ripe to revisit the production trends and key constraints facing legumes and develop smart R&D plans, keeping in view the recent developments in the fields of genomics, genetic engineering/editing, crop breeding, agronomy and technology transfer. Therefore, there was a need to document these advances that can help the research community to develop a road map. In view of this, we have brought the experts working in different areas of legumes together to document their experiences and provide a road map through this book.

Protein-rich food legumes are usually cultivated as rain-dependent crops under subsistence agriculture. Besides this, most farmers are deprived of improved seeds due to lack of interest in both public and private seed industries. These factors lead to unacceptably poor yields at the farm level. In a number of field crops, the cultivation of hybrids has resulted in quantum jump in their productivity, but by contrast in legumes, only inbred cultivars are in cultivation with poor harvests. In the last few decades, breeders are attempting to develop hybrid breeding technology in two legumes, faba bean and pigeonpea, where natural out-crossing is sufficient to support their large-scale hybrid seed production. Besides these, attempts are also being made to develop a hybrid technology in soybean, where male sterility systems have been bred, and attempts are being made to enhance the level of cross-pollination to facilitate the production of cross-pollinated seed. Of the three crops, the success has been achieved only in pigeonpea [Cajanus cajan (L.) Millsp.] where three commercial hybrids have been bred. In farmers’ fields, these hybrids produce 30–50% more yield over the local control. This review deals with breeders’ efforts towards developing hybrid technology in the three legume crops along with the major accomplishments in hybrid pigeonpea breeding.

Seed protein content (SPC) is an important grain quality trait, which impacts the nutritional importance of pigeonpea seed in the diet of over a billion people globally. The present study was carried out to determine variation in SPC and its relationships with some agronomic traits among 23 parental lines of different types of pigeonpea mapping populations. The parental lines were evaluated under field conditions during 2014-2015 growing season. A randomised complete block design in two replications was used. Data were recorded on SPC, days to first flower (DTF), plant height at maturity (PltH), number of pods per plant (NPP), number of seeds per pod (NSP), hundred-seed weight (SW) and seed yield per plant (SY). There were significant differences among genotypes for all traits. Broad-sense heritability was 0.693 for SPC but ranged from 0.519 (NPP) to 0.999 (DTF) while genetic advance was 2.4% for SPC but ranged from 1.2 % (NSP) to 141.2 % (SY), and genetic gain ranged from 11.0 % (SPC) to 230.0 % (SY). Simple correlation showed that SPC is only significantly but negatively correlated with SW (r = -0.30, P < 0.05), while path analyses revealed that SPC is negatively associated SW and NPP but positively with DTF, PltH, NSP and SY. It is concluded that genetic variation for SPC and agronomic traits exist among pigeonpea genotypes studied. The variation is accompanied by both favourable and unfavourable relationships of SPC with the agronomic traits.

Pigeonpea is an important food legume of the semi-arid tropics grown mainly under subsistence agriculture. As a first step to address the five decades-long yield stagnation, a proof-of-concept for a commercially viable CMS-based hybrid technology with high standard heterosis and fertility restoration has been demonstrated. Six generations of backcrossing and selection for male sterility, and agronomic superiority using a Cajanus cajanifolius- (A4 cytoplasm) based CMS donor (ICPA 2039) and a medium-maturity group recurrent parent ICPL 20176 (ICPB 2043) which resulted in a stable male sterile line (ICPA 2043) with near-perfect male sterility and superior agronomic traits. Following backcrossing and selections, the A-line (ICPA 2043) appeared to be morphologically similar in terms of various qualitative and quantitative traits compared to the B-line (ICPB 2043). However, differences between ICPA 2043 and ICPB 2043 were observed for days to maturity, 100-seed weight, pods plant-1, and seed weight plant-1. These differences may not be genetic but physiological. The best heterotic restorer line selected in a cross (ICPH 2671) combination restored a mean of 96.49% male fertility in 36 environments (12 locations, 3 years). Present investigation did not reveal significant G×E interaction for fertility restoration, indicating the possibility of obtaining high and stable grain yields in the pigeonpea growing areas of South and Central India.

Key message We report molecular mapping and inheritance of restoration of fertility (Rf) in A4 hybrid system in pigeonpea. We have also developed PCR-based markers amenable to low-cost genotyping to identify fertility restorer lines. Abstract Commercial hybrids in pigeonpea are based on A4 cytoplasmic male sterility (CMS) system, and their fertility restoration is one of the key prerequisites for breeding. In this context, an effort has been made to understand the genetics and identify quantitative trait loci (QTL) associated with restoration of fertility (Rf). One F2 population was developed by crossing CMS line (ICPA 2039) with fertility restorer line (ICPL 87119). Genetic analysis has shown involvement of two dominant genes in regulation of restoration of fertility. In parallel, the genotyping-by-sequencing (GBS) approach has generated ~ 33 Gb data on the F2 population. GBS data have provided 2457 single nucleotide polymorphism (SNPs) segregating across the mapping population. Based on these genotyping data, a genetic map has been developed with 306 SNPs covering a total length 981.9 cM. Further QTL analysis has provided the region flanked by S8_7664779 and S8_6474381 on CcLG08 harboured major QTL explained up to 28.5% phenotypic variation. Subsequently, sequence information within the major QTLs was compared between the maintainer and the restorer lines. From this sequence information, we have developed two PCR-based markers for identification of restorer lines from non-restorer lines and validated them on parental lines of hybrids as well as on another F2 mapping population. The results obtained in this study are expected to enhance the efficiency of selection for the identification of restorer lines in hybrid breeding and may reduce traditional time-consuming phenotyping activities. Electronic supplementary material The online version of this article (10.1007/s00122-018-3101-y) contains supplementary material, which is available to authorized users.

Chickpea (Cicer arietinum L.) and pigeonpea [Cajanus cajan L. (Millsp.)] play an important role in mitigating protein malnutrition for millions of poor vegetarians living in regions of the semi-arid tropics. Abiotic stresses such as excess and limited soil moisture (water-logging and drought), heat and chilling (high and low temperature stresses), soil salinity, and acidity are major yield constraints, as these two crops are grown mostly under rainfed conditions in risk-prone marginal and degraded lands with few or no inputs. Losses due to such stresses vary from 30% to 100% depending on their severity. The literature abounds in basic information concerning screening techniques, physiological mechanisms, and genetics of traits associated with resistance/tolerance to abiotic stresses in these two crops. However, the final outcome in terms of resistant/tolerant varieties has been far from satisfactory. This situation calls for improving selection efficiency through precise phenotyping and genotyping under high-throughput controlled conditions using modern tools of genomics. In this review, we suggest that an integrated approach combining advances from genetics, physiology, and biotechnology needs to be used for higher precision and efficiency of breeding programs aimed at improving abiotic stress tolerance in both chickpea and pigeonpea.

Adoption of pigeonpea hybrids in central and southern India is showing high impact with on‐farm yield advantages of >30%. The hybrid pigeonpea technology, the first in any legume crop, is based on a cytoplasmic‐nuclear male‐sterility (CMS) system. For a long‐term sustainability of hybrid programme, it is imperative that both nuclear diversity and cytoplasmic diversity are maintained among hybrid parents. In this context, a continuous search for new CMS‐inducing cytoplasms is necessary. This paper reports detection of maternal inheritance of male sterility in the progeny derived from a natural hybrid between a wild relative [Cajanus lineatus (W. & A.) Maesen comb. nov.] of pigeonpea and an unknown pigeonpea [Cajanus cajan (L.) Millsp.] genotype. In the present study, the male sterility was maintained up to BC7F1 generation by an advanced breeding pigeonpea line ICPL 99044. This male sterility inducing cytoplasm of C. lineatus was tagged as A6. In future, this CMS genetic stock can be used to develop a range of new pigeonpea hybrids with high yield and adaptation.

Pigeonpea [Cajanus cajan (L.) Millsp.] is an ideal pulse crop of rainfed tropics and sub-tropics due to its high nutritive value and ability to survive various biotic and abiotic stresses. Thus it has continued to be cultivated on marginal land mostly under rainfed situation where the risk of crop failure is very high. To have insurance against crop failures and harvest more food in time and space, most farmers grow pigeonpea as an intercrop with short-aged cereals and other crops. Presently, intercropping system accounts for over 70% of the pigeonpea area. However, yield of pigeonpea in this system is very low (400–500 kg/ha). The non-availability of improved cultivars adapted specifically to the intercropping environments is perhaps the major constraint that accounts for low yield. Considering the food and nutritional needs of the ever increasing population, productivity enhancement of this high-protein pulse is highly indispensable. In this review, the authors critically examine the technical difficulties encountered by breeders in developing high yielding cultivars for intercropping systems and discuss the strategies to overcome these constraints.

Long duration required for generation advancement in pigeonpea [Cajanus cajan (L.) Millsp] is one of the major bottlenecks in realizing rapid genetic gains. Therefore, a technology for rapid generation turnover is warranted to facilitate the development of new cultivars and recombinant inbred lines. Breeding of early-maturing cultivars has now opened up the possibility of rapid generation advance (RGA) in this crop. This paper reports the development of an RGA technology that integrates the germination of immature seeds with single seed descent method of breeding. The results showed that immature 35-day-old seeds can be used successfully to turn over a generation of pigeonpea with 100% seed germination. These way 3/4 successive generations can be grown within a year. The methodology presented in this study will accelerate the breeding process for breeding cultivars and develop rapidly the materials required for genomics research in pigeonpea.

Key message We report growth habit profiling following SEM, genetic mapping and QTL analysis. Highlighted CcTFL1 , a candidate for determinacy in pigeonpea, since an Indel marker derived from this gene co-segregated with Dt1 locus. Abstract Pigeonpea (Cajanus cajan) is one of the most important legume crops grown in arid and semi-arid regions of the world. It is characterized with few unique features compared with other legume species, such as Lotus, Medicago, and Glycine. One of them is growth habit, an important agronomic trait. In the present study, identification of mutations affecting growth habit accompanied by a precise analysis of phenotype has been done which will shed more light upon developmental regulation in pigeonpea. A genetic study was conducted to examine the inheritance of growth habit and a genotyping by sequencing (GBS)-based genetic map constructed using F2 mapping population derived from crossing parents ICP 5529 and ICP 11605. Inheritance studies clearly demonstrated the dominance of indeterminate (IDT) growth habit over determinate (DT) growth habit in F2 and F2:3 progenies. A total of 787 SNP markers were mapped in the genetic map of 1454 cM map length. Growth habit locus (Dt1) was mapped on the CcLG03 contributing more than 61% of total phenotypic variations. Subsequently, QTL analysis highlighted one gene, CcTFL1, as a candidate for determinacy in pigeonpea, since an Indel marker derived from this gene co-segregated with the Dt1 locus. Ability of this Indel-derived marker to differentiate DT/IDT lines was also validated on 262 pigeonpea lines. This study clearly demonstrated that CcTFL1 is a candidate gene for growth habit in pigeonpea and a user-friendly marker was developed in the present study which will allow low-cost genotyping without need of automation. Electronic supplementary material The online version of this article (doi:10.1007/s00122-017-2924-2) contains supplementary material, which is available to authorized users.

Fusarium wilt (FW) is one of the most important biotic stresses causing yield losses in pigeonpea. Genetic improvement of pigeonpea through genomics-assisted breeding (GAB) is an economically feasible option for the development of high yielding FW resistant genotypes. In this context, two recombinant inbred lines (RILs) (ICPB 2049 × ICPL 99050 designated as PRIL_A and ICPL 20096 × ICPL 332 designated as PRIL_B) and one F2 (ICPL 85063 × ICPL 87119) populations were used for the development of high density genetic maps. Genotyping-by-sequencing (GBS) approach was used to identify and genotype SNPs in three mapping populations. As a result, three high density genetic maps with 964, 1101 and 557 SNPs with an average marker distance of 1.16, 0.84 and 2.60 cM were developed in PRIL_A, PRIL_B and F2, respectively. Based on the multi-location and multi-year phenotypic data of FW resistance a total of 14 quantitative trait loci (QTLs) including six major QTLs explaining >10% phenotypic variance explained (PVE) were identified. Comparative analysis across the populations has revealed three important QTLs (qFW11.1, qFW11.2 and qFW11.3) with upto 56.45% PVE for FW resistance. This is the first report of QTL mapping for FW resistance in pigeonpea and identified genomic region could be utilized in GAB.

Pigeonpea [Cajanus cajan (L.) Millsp.] is an important rainfed pulse crop of tropics and sub-tropics, and during its long growth cycle of 6–9 months it encounters a number of biotic and abiotic stresses. The recently developed CMS-based pigeonpea hybrids have demonstrated large gains in yield and stability over the traditional inbred cultivars. In this review, the authors argue that the heterosis expressed in traits like seed germination, radicle growth, root biomass production and moisture retention during water stress confers advantages to hybrid plants in negotiating a few abiotic and biotic stresses in much better way than pure line cultivars.

A set of 102 hybrid combinations, developed by crossing three A4 CMS lines and 34 diverse testers, was evaluated to identify potential parental genotypes for breeding new high yielding cultivars. The hybrid combinations were assessed for their per se performance, standard heterosis and combining ability. Significant differences were recorded for parents versus hybrids for yield and its related traits, suggesting the presence of substantial heterotic responses. Highly significant GCA effects for yield were recorded within the female parents and testers. Relatively more number of hybrids involving ICPA 2092, as female parent, exhibited significant positive SCA values for yield, days to flower, plant height, primary branches, pods/plant, seed size and seeds/pod. A total of 45 hybrids recorded significant SCA effects for productivity. The yield superiority of hybrids over the inbred control cultivar ranged from -50.81 to 76.89%. Interestingly, 23 hybrids were also found superior to the first released pigeonpea hybrid ICPH 2671 by a margin of 5.48% to 64.31%. On the basis of their performance in hybrid combinations, the testers were classified into seven heterotic groups. The present study identified two CMS lines (ICPA 2092 and ICP 2043) and 13 testers including ICP 3525, ICPL 20196, BDN 2001-6 and BSMR 198 etc. as potential parental lines for use in breeding medium duration pigeonpea pure line and hybrid cultivars.

Pigeonpea [Cajanus cajan (L.) Millsp.] is a pulse crop cultivated in the semi‐arid regions of Asia and Africa. It is a rich source of protein and capable of alleviating malnutrition, improving soil health and the livelihoods of small‐holder farmers. Hybrid breeding has provided remarkable improvements for pigeonpea productivity, but owing to a tedious and costly seed production system, an alternative two‐line hybrid technology is being explored. In this regard, an environment‐sensitive male sterile line has been characterized as a thermosensitive male sterile line in pigeonpea precisely responding to day temperature. The male sterile and fertile anthers from five developmental stages were studied by integrating transcriptomics, proteomics and metabolomics supported by precise phenotyping and scanning electron microscopic study. Spatio‐temporal analysis of anther transcriptome and proteome revealed 17 repressed DEGs/DEPs in sterile anthers that play a critical role in normal cell wall morphogenesis and tapetal cell development. The male fertility to sterility transition was mainly due to a perturbation in auxin homeostasis, leading to impaired cell wall modification and sugar transport. Limited nutrient utilization thus leads to microspore starvation in response to moderately elevated day temperature which could be restored with auxin‐treatment in the male sterile line. Our findings outline a molecular mechanism that underpins fertility transition responses thereby providing a process‐oriented two‐line hybrid breeding framework for pigeonpea.

Pure line breeding is a resource-intensive activity that takes 10 years or more to develop a new cultivar. In some crops, conducting off-season nurseries has significantly reduced the length of the breeding cycle. This approach could not be exploited in pigeonpea [Cajanus cajan (L.) Millsp.], because traditionally it has been a photoperiod-sensitive crop that requires long periods of darkness to induce flowering. However, the recent success of breeding early maturing photoperiod-insensitive genotypes has opened up the possibility of adopting ‘speed breeding’ techniques to enable rapid generation turnover. This paper outlines a speed breeding approach that integrates the use of immature seed germination for rapid generation advancement and a “single pod descent” method of breeding. To accelerate line development, while conserving genetic variability, the approach permits four generations per year and can fast-track field evaluation of resulting homozygous lines. Therefore, the breeding strategy conserves resources and has potential to deliver new early maturing cultivars within a substantially reduced timeframe of 4–5 years.

The genetic architecture of seed protein content (SPC) and its relationships to agronomic traits in pigeonpea is poorly understood. Accordingly, five F2 populations segregating for SPC and four agronomic traits (seed weight (SW), seed yield (SY), growth habit (GH) and days to first flowering (DFF)) were phenotyped and genotyped using genotyping-by-sequencing approach. Five high-density population-specific genetic maps were constructed with an average inter-marker distance of 1.6 to 3.5 cM, and subsequently, integrated into a consensus map with average marker spacing of 1.6 cM. Based on analysis of phenotyping data and genotyping data, 192 main effect QTLs (M-QTLs) with phenotypic variation explained (PVE) of 0.7 to 91.3% were detected for the five traits across the five populations. Major effect (PVE ≥ 10%) M-QTLs included 14 M-QTLs for SPC, 16 M-QTLs for SW, 17 M-QTLs for SY, 19 M-QTLs for GH and 24 M-QTLs for DFF. Also, 573 epistatic QTLs (E-QTLs) were detected with PVE ranging from 6.3 to 99.4% across traits and populations. Colocalization of M-QTLs and E-QTLs explained the genetic basis of the significant (P

Pigeonpea [Cajanus cajan (L.) Millsp.] is traditionally cultivated as an annual crop in semi-arid regions of the world. It has a number of characteristics such as diverse maturity time, drought tolerance and natural out-crossing which makes it unique among legumes. These traits not only allow its cultivation in diverse environments and cropping systems, but also permit implementation of different breeding methods. Pigeonpea is a crop of sustainable agriculture and poor crop management, exposure to diseases and pests coupled with unpredictable rains hinder crop improvement activities. However, recently partial out-crossing has been exploited to develop cytoplasmic male-sterility (CMS) based hybrid breeding technology. Thus far, three hybrids have been released for cultivation with yield advantages of 30–50% over standard varieties. Pigeonpea R&D now also enjoys a wealth of genomics resources such as a draft genome sequence, resequencing data, candidate genes and markers associated with key traits. Genomics and breeding efforts are underway to make pigeonpea a more sustainable crop and to unlock the genetic diversity present in germplasm to develop new cultivars rapidly.

With the exception of Cajanus cajan (L.) Millspaugh (pigeonpea), the remaining species of genus Cajanus have not been domesticated. For millennia these taxa have persisted in natural habitats through self-sown seeds. These wild species are an asset for sustaining future pigeonpea breeding programmes since they contain certain traits (genes) that are necessary for encountering various breeding challenges related to crop improvement and adaptation. In this review we identify the key traits from wild Cajanus species, and discuss various physical and genetic constraints encountered in their utilization in introgression breeding. Some noteworthy achievements recorded from inter-specific breeding programmes in pigeonpea are also discussed. These include the development of (1) high protein (> 28%) genotypes (2) cytoplasmic nuclear male sterility systems (3) highly (> 95%) self-pollinating genotypes, and (4) resistance sources to sterility mosaic disease, nematodes, salinity, photo-insensitivity, pod borers, podfly, bruchids, and Phytophthora blight. To help pigeonpea breeders engaged in inter-specific breeding programmes, we suggest the division of the secondary gene pool germplasm into two sub-group/tiers on the basis of ease in hybridization.

Pigeonpea is an important source of dietary protein to over a billion people globally, but genetic enhancement of seed protein content (SPC) in the crop has received limited attention for a long time. Use of genomics-assisted breeding would facilitate accelerating genetic gain for SPC. However, neither genetic markers nor genes associated with this important trait have been identified in this crop. Therefore, the present study exploited whole genome re-sequencing (WGRS) data of four pigeonpea genotypes (~ 12X coverage) to identify sequence-based markers and associated candidate genes for SPC. By combining a common variant filtering strategy on available WGRS data with knowledge of gene functions in relation to SPC, 108 sequence variants from 57 genes were identified. These genes were assigned to 19 GO molecular function categories with 56% belonging to only two categories. Furthermore, Sanger sequencing confirmed presence of 75.4% of the variants in 37 genes. Out of 30 sequence variants converted into CAPS/dCAPS markers, 17 showed high level of polymorphism between low and high SPC genotypes. Assay of 16 of the polymorphic CAPS/dCAPS markers on an F2 population of the cross ICP 5529 (high SPC) × ICP 11605 (low SPC), resulted in four of the CAPS/dCAPS markers significantly (P

Analysis of the pigeonpea mitochondrial genome sequence identified 25 SSRs. Mononucleotide SSR motifs were the most abundant repeats followed by dinucleotide and trinucleotide repeats. Primer pairs could be designed for 24 SSRs, 23 of which were polymorphic amongst the 22 genotypes consisting of cytoplasmic male sterile (CMS or A) line, maintainer or B line and wild Cajanus species representing six different CMS systems viz., A1, A2, A4, A5, A6 and A8. These markers amplified a total of 107 alleles ranging from 2 to 10 with an average of 4.65 alleles per locus. The polymorphic information content for these markers ranged from 0.09 to 0.84 with an average of 0.52 per marker. Hence, the present study adds a novel set of 24 mitochondrial SSR markers to the markers repository in pigeonpea, which would be useful to distinguish the genotypes based on mitochondrial genome types in evolutionary and phylogenetic studies.

In cytoplasmic genetic male sterility-based (CGMS) hybrid seed production, instability of expression of male-sterility and fertility restoration across a wide range of environments are two of the major difficulties. Therefore, the present study was carried out to investigate the stability of male sterility of nine CGMS lines under three dates of sowing and the fertility restoration of 10 CGMS-based pigeonpea (Cajanus cajan (L.) Millsp.) hybrids at three different locations. Significant variability existed for pollen fertility among hybrids and sterility among cytoplasmic male sterile (CMS) lines. All the hybrids except ICPH 3494 and ICPH 3491 exhibited high (>80%) pollen fertility across locations. Hybrids ICPH 2671, ICPH 2740, and ICPH 3933 had 100% male-fertile plants across locations. All the CMS lines had completely male-sterile plants across sowing dates. The CMS lines BRG1 A, Hy3C A, BRG3 A, and TTB7 A exhibited 100% pollen sterility at different sowing dates. The pooled analysis revealed a signific...

Key message We report a likely candidate gene, CcTFL1, for determinacy in pigeonpea through candidate gene sequencing analysis, mapping, QTL analysis together with comparative genomics and expression profiling. Abstract Pigeonpea (Cajanus cajan) is the sixth most important legume crop grown on ~5 million hectares globally. Determinacy is an agronomically important trait selected during pigeonpea domestication. In the present study, seven genes related to determinacy/flowering pattern in pigeonpea were isolated through a comparative genomics approach. Single nucleotide polymorphism (SNP) analysis of these candidate genes on 142 pigeonpea lines found a strong association of SNPs with the determinacy trait for three of the genes. Subsequently, QTL analysis highlighted one gene, CcTFL1, as a likely candidate for determinacy in pigeonpea since it explained 45–96 % of phenotypic variation for determinacy, 45 % for flowering time and 77 % for plant height. Comparative genomics analysis of CcTFL1 with the soybean (Glycine max) and common bean (Phaseolus vulgaris) genomes at the micro-syntenic level further enhanced our confidence in CcTFL1 as a likely candidate gene. These findings have been validated by expression analysis that showed down regulation of CcTFL1 in a determinate line in comparison to an indeterminate line. Gene-based markers developed in the present study will allow faster manipulation of the determinacy trait in future breeding programs of pigeonpea and will also help in the development of markers for these traits in other related legume species. Electronic supplementary material The online version of this article (doi:10.1007/s00122-014-2406-8) contains supplementary material, which is available to authorized users.

To break the decades-old yield barrier in pigeonpea [Cajanus cajan (L.) Millsp.] a hybrid breeding technology was successfully developed and the first two hybrids were recently released in India. In order to produce heterotic hybrid combinations, the first logical step is the identification and selection of genetically diverse parents with favorable alleles. In this context, the concept of classifying hybrid parents into different heterotic groups was developed and successfully used in maize and later adopted in other crops. Since hybrid technology in pigeonpea is new, the authors have made the first attempt to identify heterotic groups using SCA effects of 102 crosses generated from line × tester mating and evaluated them at four locations. Based on the performance of hybrids in terms of SCA effects, seven heterotic groups were constituted. Besides this, a scheme to use this information in breeding high yielding hybrids with specific or wide adaptation is also discussed herein. Genetic diversity between lines and tester showed positive association with the heterotic pools generated on the basis of SCA.

Fertility restoration of CMS-based hybrids is an integral part of breeding hybrids and the development of new hybrid parents with desirable agronomic and market preferred traits on regular intervals is essential for sustainability of such programs. This paper reports identification of 25 male-sterility maintainers and 179 fertility restorers of A4 cytoplasm in pigeonpea (Cajanus cajan (L.) Millsp.). Multi-location evaluation of hybrids exhibited high stability for fertility restoration across diverse environments. The diversity study showed a large variation for important traits both at phenotypic as well as genetic levels. The potential use of this information in hybrid pigeonpea breeding has been discussed.

Twelve pigeonpea genotypes comprising ten hybrids and two controls were evaluated at three environments during rainy season of 2012-13, to study genotype × environment interaction for yield and related traits. Analysis of variance in each environment and on a pooled basis expressed a significant difference among genotypes for yield and yield contributing characters except for 100 seed weight. Genotype × environment (linear) interactions were found significant for days to 50% flowering, plant height, primary and secondary branches per plant, pods per plant, seeds per pod, grain yield per plant and yield (kg/ha) except days to maturity and 100 seed weight. The regression and GGE biplot methods were used for analysis. Both methods identified ICPH 2671, ICPH 2740, ICPH 3933 and ICPH 3762 as stable hybrids. The GGE biplot explained higher proportion of the mean sum of squares of the G×E interaction and was more informative with regards to environments and their genotypic performance than the regression method. Hybrids ICPH 2671, ICPH 2740, ICPH 3762 and ICPH 3933 showed stability for the yield and yield components and could be recommended for cultivation.

article i nfo Advances in next-generation sequencing and genotyping technologies have enabled generation of large-scale genomic resources such as molecular markers, transcript reads and BAC-end sequences (BESs) in chickpea, pigeonpea and groundnut, three major legume crops of the semi-arid tropics. Comprehensive transcriptome assemblies and genome sequences have either been developed or underway in these crops. Based on these resources, dense genetic maps, QTL maps as well as physical maps for these legume species have also been developed. As a result, these crops have graduated from 'orphan' or 'less-studied' crops to 'genomic resources rich' crops. This article summarizes the above-mentioned advances in genomics and genomics-assisted breeding applications in the form of marker-assisted selection (MAS) for hybrid purity assessment in pigeonpea; marker-assisted backcrossing (MABC) for introgressing QTL region for drought-tolerance related traits, Fusarium wilt (FW) resistance and Ascochyta blight (AB) resistance in chickpea; late leaf spot (LLS), leaf rust and nematode resistance in groundnut. We critically present the case of use of other modern breeding approaches like marker-assisted recurrent selection (MARS) and genomic selection (GS) to utilize the full potential of genomics-assisted breeding for developing superior cultivars with enhanced tolerance to various environmental stresses. In addition, this article recommends the use of advanced-backcross (AB-backcross) breeding and development of specialized populations such as multi-parents advanced generation intercross (MAGIC) for creating new variations that will help in developing superior lines with broadened genetic base. In summary, we propose the use of integrated genomics and breeding approach in these legume crops to enhance crop productivity in marginal environments ensuring food security in developing countries.

The hybrid pigeonpea (Cajanus cajan) breeding technology based on cytoplasmic male sterility (CMS) is currently unique among legumes and displays major potential for yield increase. CMS is defined as a condition in which a plant is unable to produce functional pollen grains. The novel chimeric open reading frames (ORFs) produced as a results of mitochondrial genome rearrangements are considered to be the main cause of CMS. To identify these CMS-related ORFs in pigeonpea, we sequenced the mitochondrial genomes of three C. cajan lines (the male-sterile line ICPA 2039, the maintainer line ICPB 2039, and the hybrid line ICPH 2433) and of the wild relative (Cajanus cajanifolius ICPW 29). A single, circular-mapping molecule of length 545.7 kb was assembled and annotated for the ICPA 2039 line. Sequence annotation predicted 51 genes, including 34 protein-coding and 17 RNA genes. Comparison of the mitochondrial genomes from different Cajanus genotypes identified 31 ORFs, which differ between lines within which CMS is present or absent. Among these chimeric ORFs, 13 were identified by comparison of the related male-sterile and maintainer lines. These ORFs display features that are known to trigger CMS in other plant species and to represent the most promising candidates for CMS-related mitochondrial rearrangements in pigeonpea.

ICRISAT scientists, working with Indian programme counterparts, developed the world's first cytoplasmic-nuclear male sterility (CMS)-based commercial hybrid in a food legume, the pigeonpea [Cajanus cajan (L.) Millsp.]. The CMS, in combination with natural outcrossing of the crop, was used to develop viable hybrid breeding technology. Hybrid ICPH 2671 recorded 47% superiority for grain yield over the control variety ‘Maruti’ in multilocation on-station testing for 4 years. In the on-farm trials conducted in five Indian states, mean yield of this hybrid (1396 kg/ha) was 46.5% greater than that of the popular cv. ‘Maruti’ (953 kg/ha). Hybrid ICPH 2671 also exhibited high levels of resistance to Fusarium wilt and sterility mosaic diseases. The outstanding performance of this hybrid has led to its release for cultivation in India by both a private seed company (as ‘Pushkal’) and a public sector university (as ‘RV ICPH 2671’). Recent developments in hybrid breeding technology and high yield advantages realized in farmers' fields have given hope for a breakthrough in pigeonpea productivity.

Complexity of yield formation is well understood by all, and there is no specific formula for breeding high-yielding cultivars. Breeders, however for a long time, have relied on selecting various individual traits, which, they thought, will contribute to yield formation directly or indirectly, and in these ways, successes have been achieved in almost all the crops. In pigeonpea, the most important individual plant traits, known to be linked to seed yield are number of pods, primary and secondary branches, and pod-bearing bunches. All these traits are quantitative in nature and have low heritability. In this paper, an attempt has been made to identify various qualitative and quantitative traits related to seed yield, quality, and those preferred for marketing and milling. A brief description about their inheritance and association with yield has also been provided to help breeders in decision-making.

Sterility mosaic disease (SMD) is one of the serious production constraints that may lead to complete yield loss in pigeonpea. Three mapping populations including two recombinant inbred lines and one F2, were used for phenotyping for SMD resistance at two locations in three different years. Genotyping-by-sequencing approach was used for simultaneous identification and genotyping of SNPs on above mentioned populations. In total, 212,464, 89,699 and 64,798 SNPs were identified in ICPL 20096 × ICPL 332 (PRIL_B), ICPL 20097 × ICP 8863 (PRIL_C) and ICP 8863 × ICPL 87119 (F2) respectively. By using high-quality SNPs, genetic maps were developed for PRIL_B (1,101 SNPs; 921.21 cM), PRIL_C (484 SNPs; 798.25 cM) and F2 (996 SNPs; 1,597.30 cM) populations. The average inter marker distance on these maps varied from 0.84 cM to 1.65 cM, which was lowest in all genetic mapping studies in pigeonpea. Composite interval mapping based QTL analysis identified a total of 10 QTLs including three major QTLs across the three populations. The phenotypic variance of the identified QTLs ranged from 3.6 to 34.3%. One candidate genomic region identified on CcLG11 seems to be promising QTL for molecular breeding in developing superior lines with enhanced resistance to SMD.

Pigeonpea [Cajanus cajan (L.) Millspaugh] is the only shrubby food legume crop with drought tolerance in the world. Insect pollinators are essential to flower pollination in cytoplasmic genetic male sterility (CGMS) pigeonpea lines, and the species, abundance, and visiting frequency of insect pollinators are the key factors for pigeonpea hybrid production. More than 46 species of insects have been reported to be flower visitors in the open field for pigeonpea production outside China, of which Megachile spp. are the major pollinators. In this study, the species, abundance, and visiting frequency of flower-visiting insects at flowering stage, as well as hybrid yield of pigeonpea, were investigated in the pigeonpea hybrid production field in Yuanmou County, Yunnan Province, China, using CGMS-based ICPH2671 hybrid. A total of 25 species of flower-visiting insects were detected, including 5 major pollinator species, Megachile velutina Sm., Megachile sp-5, Xylocopa tenuiscapa Westw., Apinae sp-1, and Megachile sp-2. At the blooming stage, the flower-visiting insects visited each primary branch at a frequency of 2.8 times per 10 min for the CGMS male sterile line, while at a frequency of 5.2 times per 10 min for the CGMS restorer line. This indicated the preference of flower-visiting insects to the flowers of restorer line. This significant difference between the male sterile and the restorer lines resulted in very similar dry seed yields of the male sterile line (383.7 g per plant) and the restorer line (357.0 g per plant). Therefore, enough pollens can been transported from the restorer line to the male sterile line by insect pollinators, even much less visiting frequency on the flowers of male sterile line compared to that of the restorer line.

Considering the increasing demand for pigeonpea [Cajanus cajan (L.) Millsp.], especially in India, breeders have realized the need to develop high-yielding, super-early maturing (

SUMMARYPigeonpea is an important legume crop of the semi-arid tropics. In India, pigeonpea is mostly grown in areas prone to waterlogging, resulting in major production losses. It is imperative to identify genotypes that show tolerance at critical crop growth stages to prevent these losses. A selection of 272 diverse pigeonpea accessions was evaluated for seed submergence tolerance for different durations (0, 120, 144, 168 and 192 h) under in vitro conditions in the laboratory. All genotypes exhibited high (0·79–0·98) survival rates for up to 120 h of submergence. After 192 h of submergence, the hybrids as a group exhibited significantly higher survival rates (0·79) than the germplasm (0·71), elite breeding lines (0·68) and commercial varieties (0·58). Ninety-six genotypes representing the phenotypic variation observed during laboratory screening were further evaluated for waterlogging tolerance at the early seedling stage using pots, and survival rates were recorded for 8 days after completion of the stress treatment. Forty-nine of these 96 genotypes, representing the phenotypic variation for waterlogging tolerance, were chosen in order to evaluate their performance under natural field conditions. The following cultivated varieties and hybrids were identified as tolerant after three levels of testing (in vitro, in pots and in the field): ICPH 2431, ICPH 2740, ICPH 2671, ICPH 4187, MAL 9, LRG 30, Maruti, ICPL 20128, ICPL 332, ICPL 20237, ICPL 20238, Asha and MAL 15. These materials can be used as sources of waterlogging tolerance in breeding programmes.

Molecular markers are the most powerful genomic tools to increase the efficiency and precision of breeding practices for crop improvement. Progress in the development of genomic resources in the leading legume crops of the semi-arid tropics (SAT), namely, chickpea (Cicer arietinum), pigeonpea (Cajanus cajan) and groundnut (Arachis hypogaea), as compared to other crop species like cereals, has been very slow. With the advances in next-generation sequencing (NGS) and high-throughput (HTP) genotyping methods, there is a shift in development of genomic resources including molecular markers in these crops. For instance, 2,000 to 3,000 novel simple sequence repeats (SSR) markers have been developed each for chickpea, pigeonpea and groundnut. Based on Sanger, 454/FLX and Illumina transcript reads, transcriptome assemblies have been developed for chickpea (44,845 transcript assembly contigs, or TACs) and pigeonpea (21,434 TACs). Illumina sequencing of some parental genotypes of mapping populations has resulted in the development of 120 million reads for chickpea and 128.9 million reads for pigeonpea. Alignment of these Illumina reads with respective transcriptome assemblies have provided more than 10,000 SNPs each in chickpea and pigeonpea. A variety of SNP genotyping platforms including GoldenGate, VeraCode and Competitive Allele Specific PCR (KASPar) assays have been developed in chickpea and pigeonpea. By using above resources, the first-generation or comprehensive genetic maps have been developed in the three legume speciesmentioned above. Analysis of phenotyping data together with genotyping data has provided candidate markers for drought-tolerance-related root traits in chickpea, resistance to foliar diseases in groundnut and sterility mosaic disease (SMD) and fertility restoration in pigeonpea. Together with these traitassociated markers along with those already available, molecular breeding programmes have been initiated for enhancing drought tolerance, resistance to fusarium wilt and ascochyta blight in chickpea and resistance to foliar diseases in groundnut. These trait-associated robust markers along with other genomic resources including genetic maps and genomic resources will certainly accelerate crop improvement programmes in the SAT legumes.

Pigeonpea (Cajanus cajan L.) is an important food legume crop of rainfed agriculture. Owing to exposure of the crop to a number of biotic and abiotic stresses, the crop productivity has remained stagnant for almost last five decades at ca. 750 kg/ha. The availability of a cytoplasmic male sterility (CMS) system has facilitated the development and release of hybrids which are expected to enhance the productivity of pigeonpea. Recent advances in genomics and molecular breeding such as marker-assisted selection (MAS) offer the possibility to accelerate hybrid breeding. Molecular markers and genetic maps are pre-requisites for deploying MAS in breeding. However, in the case of pigeonpea, only one inter- and two intra-specific genetic maps are available so far. Here, four new intra-specific genetic maps comprising 59–140 simple sequence repeat (SSR) loci with map lengths ranging from 586.9 to 881.6 cM have been constructed. Using these four genetic maps together with two recently published intra-specific genetic maps, a consensus map was constructed, comprising of 339 SSR loci spanning a distance of 1,059 cM. Furthermore, quantitative trait loci (QTL) analysis for fertility restoration (Rf) conducted in three mapping populations identified four major QTLs explaining phenotypic variances up to 24 %. To the best of our knowledge, this is the first report on construction of a consensus genetic map in pigeonpea and on the identification of QTLs for fertility restoration. The developed consensus genetic map should serve as a reference for developing new genetic maps as well as correlating with the physical map in pigeonpea to be developed in near future. The availability of more informative markers in the bins harbouring QTLs for sterility mosaic disease (SMD) and Rf will facilitate the selection of the most suitable markers for genetic analysis and molecular breeding applications in pigeonpea. Electronic supplementary material The online version of this article (doi:10.1007/s00122-012-1916-5) contains supplementary material, which is available to authorized users.

Fusarium wilt is an important disease of pigeonpea [Cajanus cajan (L.) Millsp.] and it can cause severe yield losses. Chemical control of this disease is difficult and expensive; therefore, cultivation of resistant varieties/hybrids is the most efficient strategy for enhancing the production. In the present study, by using a wilt susceptible cytoplasmic-nuclear male-sterile line and four wilt resistant fertility restorers, one dominant and one recessive gene with dominant suppressive epistatic effects were found responsible for controlling resistance to Fusarium wilt. Considering the annual losses and wide spread nature of wilt diseases in pigeonpea, it is imperative that all the inbred and hybrid cultivars have high level of resistance to this disease. The presence of dominant gene for resistance will increase the efficiency of breeding wilt resistant cultivars because it will yield greater proportion of resistant genotypes in segregating generations. In hybrid breeding also, the presence of dominant gene for wilt resistance will be an advantage. The transfer of this gene in female hybrid parents will ease the breeding of wilt resistant hybrids because this will allow the use of both wilt resistant as well as susceptible restorers in generating wilt resistant hybrid combinations.

For enhancing productivity and profitability of pigeonpea (Cajanus cajan (L.) Millsp.) a hybrid breeding technology based on a cytoplasmic nuclear male-sterility (CMS) system was developed at International Crops Research Institute for the Semi-Arid Tropics (ICRISAT). Among the elite hybrids ‘ICPH 2671’ was most out-standing with 30–35% yield advantage over local varieties. Despite its commercial release in 2010, this hybrid could not attract many growers due to its less preferred seed color. Both the parents (ICPA 2043 and ICPR 2671) of this hybrid and their crossed seeds had Greyed-orange [code no*: 167B/C (* The standard identification numbers of Royal Horticultural Society)] color. However, the commercial seeds produced on the hybrid plants surprisingly have Greyed-purple (code no: 183C) color that fetches relatively less profits. To understand the genetics of this phenomenon a cross combination was studied for seed color in F1, F2, and B1C1F1 generations. The data suggested that three independent dominant genes controlled the expression of seed coat color. The observations further suggested the presence of two dominant genes (Brsd1 and Brsd2) in the male-sterile line ‘ICPA 2043’, ‘ICPR 2671’ and another dominant gene (Brsd3) in the restorer line. In the hybrid plants genes Brsd1 and Brsd2 act in complementation with the third gene Brsd3, this also acts as a modifier. The presence of Brsd3 gene in a genotype together with Brsd1 and/or Brsd2 produces a strong inter-allelic epistatic interactions resulting in the Greyed-purple (183C) seed color. It was further postulated that the genetic constitution of ‘ICPA 2043’ is Brsd1Brsd1Brsd2Brsd2brsd3brsd3, while the genotype of the restorer line ‘ICPR 2671’ is brsd1brsd1brsd2brsd2Brsd3Brsd3.

Pigeonpea is an important legume food crop grown primarily by smallholder farmers in many semi-arid tropical regions of the world. We used the Illumina next-generation sequencing platform to generate 237.2 Gb of sequence, which along with Sanger-based bacterial artificial chromosome end sequences and a genetic map, we assembled into scaffolds representing 72.7% (605.78 Mb) of the 833.07 Mb pigeonpea genome. Genome analysis predicted 48,680 genes for pigeonpea and also showed the potential role that certain gene families, for example, drought tolerance-related genes, have played throughout the domestication of pigeonpea and the evolution of its ancestors. Although we found a few segmental duplication events, we did not observe the recent genome-wide duplication events observed in soybean. This reference genome sequence will facilitate the identification of the genetic basis of agronomically important traits, and accelerate the development of improved pigeonpea varieties that could improve food security in many developing countries.

SUMMARYPigeonpea is an important rainfed pulse crop grown in the rainy season that is subject to waterlogging. There are not many sources of waterlogging tolerance available; therefore the mini core pigeonpea germplasm (n=146) were screened, along with a few genotypes already reported to exhibit tolerance. Five trials were conducted starting at 40 and 50 days after sowing (DAS) in 2008, and at 40, 62 and 76 DAS in 2009. The mortality rate in any trial depended on the vapour pressure deficits (VPD) that prevailed during waterlogging and the recovery periods. There were large and highly significant variations due to genotype and to genotype×trial interactions. The heritability of individual trials ranged from 0·27 to 0·75, while it was 0·40 when all the trials were considered together. The survival counts were grouped into representative groups using a hierarchical cluster analysis, which yielded five distinctive groups. The highly tolerant group, with above-average survival means in all five trials, comprised 24 accessions. None of the previously tested or control entries appeared in this group. The sensitive entries comprised 37 accessions including ICP 7035, ICP 8338 and ICP 13562, which were known to be sensitive from previous reports. The tolerant group comprised 39 accessions, moderately tolerant 42 and moderately sensitive 18. Survival during waterlogging and a rapid recovery are considered equally important for categorizing the genotypes and their further use.