Cajanus cajan (L.) Millsp. commonly known as pigeonpea, red gram or gungo pea is an important grain legume crop, particularly in rain-fed agricultural regions in the semi-arid tropics, including Asia, Africa and the Caribbean. This paper provides a baseline for the study of the domestication and early history of C. cajan, through reviewing its modern wild distribution, seed morphometrics of wild and domesticated populations, historical linguistics and the archaeological record. The distribution of wild populations, including published records and additional herbarium collections, suggest that the wild habitats of pigeonpea were at the interface of the forest-edge areas and more open savanna plains in eastern Peninsular India (e.g. Telangana, Chattisgarh, Odisha). Early archaeological finds presented here have been recovered from both the Southern peninsula and Odisha. Historical linguistic data suggests early differentiation into longer and shorter growing season varieties, namely arhar and tuar types, in prehistory. Pigeonpea had spread to Thailand more than 2000 years ago. Measurements of seeds from modern populations provide a baseline for studying domestication from archaeological seeds. Available measurements taken on archaeological Cajanus spp. suggest that all archaeological collections thus far fall into a domesticated Length:Width ratio, while they may also pick up the very end of the trend towards evolution of larger size (the end of the domestication episode) between 3700 and 3200 years BP. This suggests a trend over time indicating selection under domestication had begun before 3700 years ago and can be inferred to have started 5000-4500 years ago.

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.

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Fusarium wilt (FW) and sterility mosaic diseases (SMD) are key biotic constraints to pigeonpea production. Occurrence of these two diseases in congenial conditions is reported to cause complete yield loss in susceptible pigeonpea cultivars. Various studies to elucidate genomic architecture of the two traits have revealed significant marker–trait associations for use in breeding programs. However, these DNA markers could not be used effectively in genomics-assisted breeding for developing FW and SMD resistant varieties primarily due to pathogen variability, location or background specificity, lesser phenotypic variance explained by the reported QTL and cost-inefficiency of the genotyping assays. Therefore, in the present study, a novel approach has been used to develop a diagnostic kit for identification of suitable FW and SMD resistant lines. This kit was developed with 10 markers each for FW and SMD resistance. Investigation of the diversity of these loci has shown the role of different alleles in different resistant genotypes. Two genes (C.cajan_03691 and C.cajan_18888) for FW resistance and four genes (C.cajan_07858, C.cajan_20995, C.cajan_21801 and C.cajan_17341) for SMD resistance have been identified. More importantly, we developed a customized and cost-effective Kompetitive allele-specific PCR genotyping assay for the identified genes in order to encourage their downstream applications in pigeonpea breeding programs. The diagnostic marker kit developed here will offer great strength to pigeonpea varietal development program, since the resistance against these two diseases is essentially required for nominating an improved line in varietal release pipeline.

Seed traits present important breeding targets for enhancing grain yield and quality in various grain legume crops including pigeonpea. The present study reports significant genetic variation for six seed traits including seed length (SL), seed width (SW), seed thickness (ST), seed weight (SWT), electrical conductivity (EC) and water uptake (WU) among Cajanus cajan (L.) Millspaugh acc. ICPL 20340 and Cajanus scarabaeoides (L.) Thouars acc. ICP 15739 and an F2 population derived from this interspecific cross. Maximum phenotypic values recorded for the F2 population were higher than observed in the parent ICPL 20340 [F2 max vs ICPL 20340: SW (7.05 vs 5.38), ST (4.63 vs 4.51), EC (65.17 vs 9.72), WU (213.17 vs 109.5)], which suggested contribution of positive alleles from the wild parent, ICP 15739. Concurrently, to identify the QTL controlling these seed traits, we assayed two parents and 94 F2 individuals with 113 polymorphic simple sequence repeat (SSR) markers. In the F2 population, 98 of the 113 SSRs showed Mendelian segregation ratio 1:2:1, whereas significant deviations were observed for 15 SSRs with their χ 2 values ranging between 6.26 and 20.62. A partial genetic linkage map comprising 83 SSR loci was constructed. QTL analysis identified 15 marker-trait associations (MTAs) for seed traits on four linkage groups i.e. LG01, LG02, LG04 and LG05. Phenotypic variations (PVs) explained by these QTL ranged from 4.4 (WU) to 19.91% (EC). These genomic regions contributing significantly towards observed variability of seed traits would serve as potential candidates for future research that aims to improve seed traits in pigeonpea.