C. V. Sameer Kumar

Association of nad7a Gene with Cytoplasmic Male Sterility in Pigeonpea

Cytoplasmic male sterility (CMS) has been exploited in the commercial pigeonpea [Cajanus cajan (L.) Millsp.] hybrid breeding system; however, the molecular mechanism behind this system is unknown. To understand the underlying molecular mechanism involved in A4 CMS system derived from C. cajanifolius (Haines) Maesen, 34 mitochondrial genes were analyzed for expression profiling and structural variation analysis between CMS line (ICRISAT Pigeonpea A line, ICPA 2039) and its cognate maintainer (ICPB 2039). Expression profiling of 34 mitochondrial genes revealed nine genes with significant fold differential gene expression at P ≤ 0.01, including one gene, nad4L, with 1366‐fold higher expression in CMS line as compared with the maintainer. Structural variation analysis of these mitochondrial genes identified length variation between ICPA 2039 and ICPB 2039 for nad7a (subunit of nad7 gene). Sanger sequencing of nad4L and nad7a genes in the CMS and the maintainer lines identified two single nucleotide polymorphisms (SNPs) in upstream region of nad4L and a deletion of 10 bp in nad7a in the CMS line. Protein structure evaluation showed conformational changes in predicted protein structures for nad7a between ICPA 2039 and ICPB 2039 lines. All above analyses indicate association of nad7a gene with the CMS for A4 cytoplasm in pigeonpea. Additionally, one polymerase chain reaction (PCR) based Indel marker (nad7a_del) has been developed and validated for testing genetic purity of A4 derived CMS lines to strengthen the commercial hybrid breeding program in pigeonpea.

Plant growth-promotion and biofortification of chickpea and pigeonpea through inoculation of biocontrol potential bacteria, isolated from organic soils

Seven strains of bacteria [Pseudomonas plecoglossicida SRI-156, Brevibacterium antiquum SRI-158, Bacillus altitudinis SRI-178, Enterobacter ludwigii SRI-211, E. ludwigii SRI-229, Acinetobacter tandoii SRI-305 and Pseudomonas monteilii SRI-360; demonstrated previously for control of charcoal rot disease in sorghum and plant growth-promotion (PGP) in rice] were evaluated for their PGP and biofortification traits in chickpea and pigeonpea under field conditions. When treated on seed, the seven selected bacteria significantly enhanced the shoot height and root length of both chickpea and pigeonpea over the un-inoculated control. Under field conditions, in both chickpea and pigeonpea, the plots inoculated with test bacteria enhanced the nodule number, nodule weight, root and shoot weights, pod number, pod weight, leaf weight, leaf area and grain yield over the un-inoculated control plots. Among the seven bacteria, SRI-229 was found to significantly and consistently enhance all the studied PGP and yield traits including nodule number (24 and 36%), nodule weight (11 and 44%), shoot weight (22 and 20%), root weight (23 and 16%) and grain yield (19 and 26%) for both chickpea and pigeonpea, respectively. When the harvested grains were evaluated for their mineral contents, iron (up to 18 and 12%), zinc (up to 23 and 5%), copper (up to 19 and 8%), manganese (up to 2 and 39%) and calcium (up to 22 and 11%) contents in chickpea and pigeonpea, respectively, were found enhanced in test bacteria inoculated plots over the un-inoculated control plots. This study further confirms that the selected bacterial isolates not only have the potential for PGP in cereals and legumes but also have the potential for biofortification of mineral nutrients.

Construction of genotyping-by-sequencing based high-density genetic maps and QTL mapping for fusarium wilt resistance in pigeonpea

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.

Genomics, genetics and breeding of tropical legumes for better livelihoods of smallholder farmers

Abstract Legumes are important components of sustainable agricultural production, food, nutrition and income systems of developing countries. In spite of their importance, legume crop production is challenged by a number of biotic (diseases and pests) and abiotic stresses (heat, frost, drought and salinity), edaphic factors (associated with soil nutrient deficits) and policy issues (where less emphasis is put on legumes compared to priority starchy staples). Significant research and development work have been done in the past decade on important grain legumes through collaborative bilateral and multilateral projects as well as the CGIAR Research Program on Grain Legumes (CRP‐GL). Through these initiatives, genomic resources and genomic tools such as draft genome sequence, resequencing data, large‐scale genomewide markers, dense genetic maps, quantitative trait loci (QTLs) and diagnostic markers have been developed for further use in multiple genetic and breeding applications. Also, these mega‐initiatives facilitated release of a number of new varieties and also dissemination of on‐the‐shelf varieties to the farmers. More efforts are needed to enhance genetic gains by reducing the time required in cultivar development through integration of genomics‐assisted breeding approaches and rapid generation advancement.

Development and Application of High-Density Axiom SNP Array with 56K SNPs to Understand the Genome Architecture of Released Cultivars and Founder Genotypes

Axiom Cajanus SNP array revealed genetic architecture and temporal diversity in pigeonpea varieties.

Development of sequence-based markers for seed protein content in pigeonpea

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 < 0.05) co-segregated with SPC. In summary, four markers derived from mutations in four genes will be useful for enhancing/regulating SPC in pigeonpea crop improvement programs.

Genetic variability and correlation in pigeonpea genotypes

Forty nine pigeon pea genotypes were evaluated at Agricultural Research Station Tandur during kharif 2015-16. Genotypes were grouped into six clusters based on Mahalonobis D statistics. Days to maturity contributed to maximum genetic divergence followed by days to 50% flowering. Maximum inter cluster distance was observed between clusters II and VI and intra cluster distance in cluster I and II. Genotypes in cluster V recorded highest mean values for number of secondary branches/plant and number of pods/plant and seed yield. Broad sense heritability estimates were highest for days to maturity and days to 50% flowering. Significant and positive genotypic and phenotypic correlation was observed between seed yield and number of pods/plant and number of secondary branches/plant. The range of GCV observed was 4.55 to 22.07% for the traits under study indicating the extent of variability present among the pigeon pea genotypes. Path coefficient analysis revealed that days to maturity exhibited maximum direct effect followed by number of pods/plant.

Botanical Description of Pigeonpea [Cajanus Cajan (L.) Millsp.]

Pigeonpea [Cajanus cajan (L.) Millspaugh] is an important legume crop of the papilionaceae family. It is an often cross-pollinated crop, and breeding principles of both self and cross-pollinated crops are highly effective in its genetic enhancement. Pigeonpea is a hard woody shrub, extensively adaptable to a range of soil types, temperature, and rainfall. It has a deep taproot system extending up to two meters and can grow to a height of four meters. Pigeonpea roots form a symbiotic association with Brady rhizobium spp. and perform biological nitrogen fixation. The branching pattern of stem may vary from bush type to compact upright type and is of determinate, semi-determinate, and non-determinate type based on the flowering pattern. The primary leaves are simple, opposite, and caduceus, while the latter ones are pinnately trifoliate with lanceolate to elliptical leaflets. Pigeonpea flowers are zygomorphic, borne on terminal or auxiliary racemes and are normally yellow in color with some variations. It has ten stamens in diadelphous condition with light or dark yellow anthers. The ovary is superior with a long style attached to a thickened, incurved, and swollen stigma. Pigeonpea is an often cross-pollinated crop with an average of 20% cross-pollination. The fruit of pigeonpea is called pod, which is of various colors, with and without deep constrictions. Seeds (with 20–22% proteins and amino acids) can be round or lens shaped, in shades of white and brown color with yellow color cotyledon. Pigeonpea is a widely consumed multi-utility pulse crop, thus the knowledge about the crop botany is vital for modifying it according to future challenges and goals.

Technologies for Intensification of Production and Uses of Grain Legumes for Nutrition Security

Malnutrition resulting from intake of food poor in nutritional value, particularly lacking in micronutrients, has been recognized as a serious health problem in developing countries including India. Nutritional security is a priority for India. Crop diversification in agriculture contributes to balanced diet and nutritional security. Production intensification of nutrient-dense crops, contributes to their increased production, and consequently enhances their accessibility at affordable prices to meet nutritional security. Grain legumes produce nutrient-dense grains rich in proteins, vitamins, minerals and micronutrients essential for growth and development. However, cultivation of grain legumes is often neglected resulting in poor production in the country, and consequently poor access to legumes at affordable prices. Pigeonpea or red gram (Cajanus cajan L.), chickpea or bengal gram (Cicer arietinum L.) and groundnut (Arachis hypogaea L.), the three nutritious grain legumes are grown widely across the country and are major constituents of Indian diets. They are climate- resilient crops adapted to water-limiting conditions making them choice crops for cultivation in adverse conditions. Policy options for promoting cultivation and increased production of pigeon pea, chickpea and groundnut are needed. Technology options for intensification of their cultivation include improved cultivars of grain legumes with enhanced adaptation and nutritional properties, their processing, plugging post-harvest and storage losses, and development of alternative food products. The chapter discusses the contribution of agriculture to nutritional security and the need to diversify cultivation of crops to include nutrient-dense grain legumes, and intensification of their cultivation to achieve their enhanced production and productivity. The scope to develop bio-fortified grain legumes is also discussed. Some countries have successfully harnessed the potential of processed grain legumes for use as food supplements for children and elderly, as well as to prepare readyto-use-therapeutic-food products to treat acute malnutrition.