Whole chloroplast genome-specific non-synonymous SNPs reveal the presence of substantial diversity in the pigeonpea mini-core collection

To unravel the plastid genome diversity among the cultivated groups of the pigeonpea germplasm, we characterized the SNP occurrence and distribution of 142 pigeonpea mini-core collections based on their reference-based assembly of the chloroplast genome. A total of 8921 SNPs were found, which were again filtered and finally 3871 non-synonymous SNPs were detected and used for diversity estimates. These 3871 SNPs were classified into 12 groups and were present in only 44 of the 125 genes, demonstrating the presence of a precise mechanism for maintaining the whole chloroplast genome throughout evolution. The Acetyl-CoA carboxylase D gene possesses the maximum number of SNPs (12.29%), but the Adenosine Tri-Phosphate synthatase cluster genes (atpA, atpB, atpE, atpF, atpH, and atpI) altogether bear 43.34% of the SNPs making them most diverse. Various diversity estimates, such as the number of effective alleles (1.013), Watterson's estimate (0.19), Tajima's D ( - 3.15), Shannon's information index (0.036), suggest the presence of less diversity in the cultivated gene pool of chloroplast genomes. The genetic relatedness estimates based on pairwise correlations were also in congruence with these diversity descriptors and indicate the prevalence of rare alleles in the accessions. Interestingly, no stratification was observed either through STRUCTURE, PCoA, or phylogenetic analysis, indicating the common origin of the chloroplast in all the accessions used, irrespective of their geographical distribution. Further 6194 Cleaved Amplified Polymorphic Sequences (CAPS) markers for 531 SNPs were developed and validated in a selected set of germplasm. Based on these results, we inferred that all of the cultivated gene pools of pigeonpea have a common origin for the chloroplast genome and they possess less diversity in protein-coding regions, indicating a stable and evolved plastid genome. At the same time, all diversity analysis indicates the occurrence of rare alleles, suggesting the suitability of the mini-core collection in future pigeonpea improvement programs. In addition, the development of chloroplast genome-based CAPS markers would have utility in pigeonpea breeding programs.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-023-03785-8.

Introgression of productivity enhancing traits, resistance to pod borer and Phytopthora stem blight from Cajanus scarabaeoides to cultivated pigeonpea

The study aimed at introgression of productivity enhancing traits and resistance to pod borer and Phytophthora stem blight from wild to cultivated pigeonpea through an inter-specific cross between Cajanus scarabaeoides (ICP 15683) and C. cajan (ICPL 20329). Progenies derived from the direct segregating (without backcross) population and backcross population were evaluated for yield and yield contributing traits namely fruiting branches and pods plant^-1 and 100-seed weight. Introgressed progenies having higher fruiting branches, pods and yield plant^-1 compared to the cultivated parent were identified in both populations. A few progenies with significantly shorter plant height, early flowering and early maturity as compared to both cultivated and wild parents were also recovered in both populations. Progenies from both the populations were identified with higher resistance to pod borer and Phytophthora stem blight. However, some introgressed progenies having lower seed weight and seeds per pod were also recovered. The promising progenies are currently being used in the breeding programme to develop cultivars with improved productivity and resistance to pod borer and Phytophthora stem blight.