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

Abstract

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 F 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.

Seed protein content and its relationships with agronomic traits in pigeonpea is controlled by both main and epistatic effects QTLs

“…The three CcLGs (CcLG02, CcLG03 and CcLG11) also contained M-QTLs with the highest PVE than M-QTLs on the other CcLGs suggesting their relative importance in harbouring genomic regions governing SPC in the pigeonpea. The localisation of the major M-QTLs on CcLG02 in three of the five populations in the present study could be supported by the detection on the same chromosome of some genes known for their functional role in seed storage protein accumulation such as NADH-GOGAT 25 , or for their location in the vicinity of QTL regions associated with variability of SPC in plants 37 . By projecting the population specific M-QTLs to the consensus genetic map, six consensus genomic regions, each comprising M-QTLs for SPC from two to four populations were generated.…”

“…Across populations, the number of E-QTLs detected also varied by trait. The pattern of contributions of M-QTLs vs E-QTLs to phenotypic variation for the studied traits seemed to be highly genetic background-dependent as has been frequently reported in other crops 62-65. In an earlier study, we reported a number of putative candidate gene-based nsSNP for SPC, some of which significantly cosegregated with the trait in an F 2 validation population, ICP 5529 × ICP 11605 25 . Similarly, Saxena et al 12 developed a CcFTL1 gene-based Indel marker whose cosegregation with the determinate GH locus Dt1 was validated in the same F 2 population.…”

“…In pigeonpea, QTLs have been mapped for plant type and earliness including days to flowering and growth habit 10,12,35 and disease resistance 13 . However, such studies have lacked for SPC and it is only till recently that we developed gene-derived sequence-based markers using whole genome resequencing of pigeonpea parental lines 25 . Genomic regions associated with SPC and correlated traits offer opportunity to develop varieties with enhanced SPC and stable yield using genomics-assisted breeding approaches.…”

“…Sun drying was done for one week before threshing and another one week after threshing to ensure uniform reduction in seed moisture content. Seed protein content was measured as described in Obala et al 25,67 . Besides SPC, data were also recorded for SW in grams, SY in grams per plant, DFF, and GH scored as determinate or indeterminate.…”

Neglected and Underutilized Legume Crops: Improvement and Future Prospects

“…Genetic and breeding efforts to improve the underutilized and neglected legume crops in architecture, period of maturation, yield, and nutritional contents have not recorded commiserate level of success as expected [88,89]. Traditional hybridization and other breeding techniques, though have been used for some desired intentions, are yet to translate to desired results.…”