A mapping population of recombinant inbred lines (RILs) derived from TMV 2 and its mutant, TMV 2-NLM was employed for mapping important taxonomic and productivity traits using genic and non-genic transposable element markers in peanut. Single nucleotide polymorphism and copy number variation using RAD-Sequencing data indicated very limited polymorphism between TMV 2 and TMV 2-NLM. But phenotypically they differed significantly for many taxonomic and productivity traits. Also, the RIL population showed significant variation for a few additional agronomic traits. A genetic linkage map of 1,205.66 cM was constructed using 91 genic and non-genic Arachis hypogaea transposable element (AhTE) markers. Using single marker analysis and QTL analysis, the markers with high phenotypic variance explained (PVE) were identified for branching pattern (32.3%), number of primary and secondary branches (19.9% and 28.4%, respectively), protein content (26.4%), days to 50% flowering (22.0%), content of oleic acid (15.1%), test weight (13.6%) and pod width (12.0%). Three genic markers (AhTE0357, AhTE0391, AhTE0025) with Arachis hypogaea miniature inverted-repeat transposable element (AhMITE1) activity in the genes Araip.TG1BL (B02 chromosome), Aradu.7N61X (A09 chromosome) and Aradu.7065G (A07 chromosome), respectively showed strong linkage with these taxonomic, productivity and quality traits. Since TMV 2 and TMV 2-NLM differed subtly at DNA level, the background noise in detecting the marker-trait associations was minimum; therefore, the markers identified in this study for the taxonomic and productivity traits may be significant and useful in peanut molecular breeding.

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.

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Pigeonpea is one of the important pulse crops grown in many states of India and plays a major role in sustainable food and nutritional security for the smallholder farmers. In order to overcome the productivity barrier the Translational Pigeonpea Genomics Consortium (TPGC) was established, representing research institutes from six different states (Andhra Pradesh, Karnataka, Madhya Pradesh, Maharashtra, Telangana, and Uttar Pradesh) of India. To enhance pigeonpea productivity and production the team has been engaged in deploying modern genomics approaches in breeding and popularizing modern varieties in farmers’ fields. For instance, new genetic stock has been developed for trait mapping and molecular breeding initiated for enhancing resistance to fusarium wilt and sterility mosaic disease in 11 mega varieties of pigeonpea. In parallel, genomic segments associated with cleistogamous flower, shriveled seed, pods per plant, seeds per pod, 100 seed weight, and seed protein content have been identified. Furthermore, 100 improved lines were evaluated for yield and desirable traits in multi-location trials in different states. Furthermore, a total of 303 farmers’ participatory varietal selection (FPVS) trials have been conducted in 129 villages from 15 districts of six states with 16 released varieties/hybrids. Additionally, one line (GRG 152 or Bheema) from multi-location trials has been identified by the All India Coordinated Research Project on Pigeonpea (AICRP-Pigeonpea) and released for cultivation by the Central Variety Release Committee (CVRC). In summary, the collaborative efforts of several research groups through TPGC is accelerating genetics gains in breeding plots and is expected to deliver them to pigeonpea farmers to enhance their income and improve livelihood.

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