Abstract
With an objective of identifying the genomic regions for productivity and quality traits in peanut, a recombinant inbred line (RIL) population developed from an elite variety, TMV 2 and its ethyl methane sulfonate (EMS)-derived mutant was phenotyped over six seasons and genotyped with genotyping-by-sequencing (GBS), Arachis hypogaea transposable element (AhTE) and simple sequence repeats (SSR) markers. The genetic map with 700 markers spanning 2,438.1 cM was employed for quantitative trait loci (QTL) analysis which identified a total of 47 main-effect QTLs for the productivity and oil quality traits with the phenotypic variance explained (PVE) of 10–52% over the seasons. A common QTL region (46.7–50.1 cM) on Ah02 was identified for the multiple traits, such as a number of pods per plant (NPPP), pod weight per plant (PWPP), shelling percentage (SP), and test weight (TW). Similarly, a QTL (7.1–18.0 cM) on Ah16 was identified for both SP and protein content (PC). Epistatic QTL (epiQTL) analysis revealed intra- and inter-chromosomal interactions for the main-effect QTLs and other genomic regions governing these productivity traits. The markers identified by a single marker analysis (SMA) mapped to the QTL regions for most of the traits. Among the five potential candidate genes identified for PC, SP and oil quality, two genes (Arahy.7A57YA and Arahy.CH9B83) were affected by AhMITE1 transposition, and three genes (Arahy.J5SZ1I, Arahy.MZJT69, and Arahy.X7PJ8H) involved functional single nucleotide polymorphisms (SNPs). With major and consistent effects, the genomic regions, candidate genes, and the associated markers identified in this study would provide an opportunity for gene cloning and genomics-assisted breeding for increasing the productivity and enhancing the quality of peanut.
Highlights
Peanut or groundnut (Arachis hypogaea L. 2n = 4x = 40) is an important oilseed, legume food, and fodder crop, which, in 2019, was cultivated globally on an area of 29.5 million ha with a production of 48.7 million tons and a productivity of 1,647 kg/ha
oleic acid content (OLE) was positively correlated with pod weight per plant (PWPP) (0.03∗-0.11∗) and test weight (TW) (0.09∗-0.12∗∗), it was negatively correlated with number of pods per plant (NPPP) (−0.10∗ to −0.18∗∗) and shelling percentage (SP) (−0.09∗ to −0.15∗∗), protein content (PC) (−0.32∗∗ to −0.34∗∗), oil content (OIL) (−0.03∗ to −0.29∗∗), and linoleic acid content (LIN) (−0.64∗∗ to −0.96∗∗) (Supplementary Table 3)
The recombinant inbred line (RIL) population derived from TMV 2 and TMV 2-NLM was used for constructing the Arachis hypogaea transposable element (AhTE) markerbased genetic map and identifying the quantitative trait loci (QTL) for important taxonomic and productivity traits (Hake et al, 2017)
Summary
Over half of the peanut produce goes for oil extraction while the remaining is consumed as raw and processed food. In India, over 80% of the produce was used for oil extraction in the past. It has reduced to
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