Genetic Patterns of Domestication in Pigeonpea (Cajanus cajan (L.) Millsp.) and Wild Cajanus Relatives

Pigeonpea (Cajanus cajan) is an annual or short-lived perennial food legume of acute regional importance, providing significant protein to the human diet in less developed regions of Asia and Africa. Due to its narrow genetic base, pigeonpea improvement is increasingly reliant on introgression of valuable traits from wild forms, a practice that would benefit from knowledge of its domestication history and relationships to wild species. Here we use 752 single nucleotide polymorphisms (SNPs) derived from 670 low copy orthologous genes to clarify the evolutionary history of pigeonpea (79 accessions) and its wild relatives (31 accessions). We identified three well-supported lineages that are geographically clustered and congruent with previous nuclear and plastid sequence-based phylogenies. Among all species analyzed Cajanus cajanifolius is the most probable progenitor of cultivated pigeonpea. Multiple lines of evidence suggest recent gene flow between cultivated and non-cultivated forms, as well as historical gene flow between diverged but sympatric species. Evidence supports that primary domestication occurred in India, with a second and more recent nested population bottleneck focused in tropical regions that is the likely consequence of pigeonpea breeding. We find abundant allelic variation and genetic diversity among the wild relatives, with the exception of wild species from Australia for which we report a third bottleneck unrelated to domestication within India. Domesticated C. cajan possess 75% less allelic diversity than the progenitor clade of wild Indian species, indicating a severe “domestication bottleneck” during pigeonpea domestication

PCR amplification of black gram genic-SSR marker VMgSSR-78 in related <i>Vigna</i> species.

<p>PCR amplification of black gram genic-SSR marker VMgSSR-78 in related <i>Vigna</i> species.</p

Distribution of transcript contig length assembled from black gram transcriptome sequencing.

<p>Distribution of transcript contig length assembled from black gram transcriptome sequencing.</p

<i>De novo</i> Assembly, Characterization of Immature Seed Transcriptome and Development of Genic-SSR Markers in Black Gram [<i>Vigna mungo</i> (L.) Hepper]

<div><p>Black gram [<i>V</i>. <i>mungo</i> (L.) Hepper] is an important legume crop extensively grown in south and south-east Asia, where it is a major source of dietary protein for its predominantly vegetarian population. However, lack of genomic information and markers has become a limitation for genetic improvement of this crop. Here, we report the transcriptome sequencing of the immature seeds of black gram cv. TU94-2, by Illumina paired end sequencing technology to generate transcriptome sequences for gene discovery and genic-SSR marker development. A total of 17.2 million paired-end reads were generated and 48,291 transcript contigs (TCS) were assembled with an average length of 443 bp. Based on sequence similarity search, 33,766 TCS showed significant similarity to known proteins. Among these, only 29,564 TCS were annotated with gene ontology (GO) functional categories. A total number of 138 unique KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways were identified, of which majority of TCS are grouped into purine metabolism (678) followed by pyrimidine metabolism (263). A total of 48,291 TCS were searched for SSRs and 1,840 SSRs were identified in 1,572 TCS with an average frequency of one SSR per 11.9 kb. The tri-nucleotide repeats were most abundant (35%) followed by di-nucleotide repeats (32%). PCR primer pairs were successfully designed for 933 SSR loci. Sequences analyses indicate that about 64.4% and 35.6% of the SSR motifs were present in the coding sequences (CDS) and untranslated regions (UTRs) respectively. Tri-nucleotide repeats (57.3%) were preferentially present in the CDS. The rate of successful amplification and polymorphism were investigated using selected primers among 18 black gram accessions. Genic-SSR markers developed from the Illumina paired end sequencing of black gram immature seed transcriptome will provide a valuable resource for genetic diversity, evolution, linkage mapping, comparative genomics and marker-assisted selection in black gram.</p></div

Distribution of genic-SSR motifs in the coding sequence and untranslated region (UTRs) of black gram transcriptome sequences.

<p>Distribution of genic-SSR motifs in the coding sequence and untranslated region (UTRs) of black gram transcriptome sequences.</p

Distribution and frequency of SSR nucleotide classes among different nucleotide types found in the transcriptome sequence.

<p>Distribution and frequency of SSR nucleotide classes among different nucleotide types found in the transcriptome sequence.</p

Blast hit distribution of black gram TCS showing similarity with known proteins in non-redundant (nr) database available at NCBI using BLASTx algorithm with an E value threshold of 10^–5.

<p>Blast hit distribution of black gram TCS showing similarity with known proteins in non-redundant (nr) database available at NCBI using BLASTx algorithm with an E value threshold of 10^–5.</p

PCR amplification using genic-SSR marker VMgSSR-30 in 18 black gram genotypes.

<p>PCR amplification using genic-SSR marker VMgSSR-30 in 18 black gram genotypes.</p

GO Annotation analysis for contigs from <i>V</i>. <i>mungo</i>.

<p>GO Annotation analysis for contigs from <i>V</i>. <i>mungo</i>.</p