Genotyping-by-Sequencing Based Genetic Mapping Identified Major and Consistent Genomic Regions for Productivity and Quality Traits in Peanut

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.

Genetic mapping of tolerance to iron deficiency chlorosis in peanut (Arachis hypogaea L.)

“…Of the ve major QTL, four were clustered in two genomic regions; a 24.5 cM region on Ah12 chromosome with 300 predicted genes carried one QTL each for VCR90 and SCMR90, and a 19 cM region on chromosome Ah13 with 259 predicted genes carried one QTL each for VCR90 and SCMR30. The cluster 2 on Ah13 was consistent as it was also identi ed for VCR90 by Pattanashetti et al (2020), while Pandey et al (2021) identi ed a QTL cluster on Ah13 for VCR30, SCMR60 and SCMR90. These regions can be the targets for further ne-mapping.…”

“…Recent genomics studies using the RIL population of TAG 24 × ICGV 86031 and a map of 191 SSR markers identi ed two major QTLs for VCR with the highest PVE of 31.8% and a single major QTL for SCMR with a PVE of 11.0% (Pattanashetti et al 2020). Subsequently, Pandey et al (2021) improved the genetic map for TAG 24 × ICGV 86031 using 1028 SNP loci genotyped with a high-density 58K "Axiom_Arachis" array and 177 SSR markers. The genome-wide QTL analysis identi ed a single major main-effect QTL for VCR with a PVE of 33.9% and two major main-effect QTLs for SCMR with the highest PVE of 22.4%.…”

“…The RIL population derived from TMV 2 and TMV 2-NLM has demonstrated its utility in mapping complex traits (Hake et al 2017, Jadhav et al 2021) since the latter parent is an EMS-derived mutant of the former, and helps in subtracting out a major genomic portion common to both the parents. Therefore, an effort was made in this study to map the genomic regions governing IDC tolerance using a RIL population derived from TMV 2 and TMV 2-NLM which was phenotyped during the rainy seasons of 2019 and 2020 in the iron-de cient calcareous plots, and a dense genetic map of GBS-derived SNP, AhTE and SSR markers.…”

Genome-Wide Characterization of Ascorbate Peroxidase Gene Family in Peanut (Arachis hypogea L.) Revealed Their Crucial Role in Growth and Multiple Stress Tolerance

“…Cultivated peanut is widely known as an essential oilseed, protein-enrich food crop worldwide and retains important breeding traits during domestication (Zhuang et al, 2019;Bohra et al, 2022). Even so, peanut production is still substantially influenced by numerous biotic and abiotic factors (Agarwal et al, 2018;Gangurde et al, 2020Gangurde et al, , 2021Kumar et al, 2020;Shasidhar et al, 2020;Sinha et al, 2020;Jadhav et al, 2021;Pandey et al, 2021;Soni et al, 2021;Aravind et al, 2022;Bomireddy et al, 2022;Liu et al, 2022;Patel et al, 2022). When plants are exposed to diverse abiotic and biotic factors, APX enzyme as a primary marker can quickly eliminate unnecessary H 2 O 2 (i.e., ROS scavenging) from plant cells by adjusting several physiological and biochemical activities to safeguard cells from the noxiousness of overproduction of ROS (Das and Roychoudhury, 2014;Mittler, 2017;Hasanuzzaman et al, 2020Hasanuzzaman et al, , 2021.…”

“…Cultivated peanut/groundnut (A. hypogaea L.), an allotetraploid crop, is one of the most valuable and economic oilseed food crops globally (Agarwal et al, 2018;Bertioli et al, 2019;Chen X. et al, 2019;Zhuang et al, 2019). This crop is being widely cultivated in the tropical and subtropical regions globally; however, several abiotic and biotic factors significantly affect its growth and production, including many important agronomic traits (Agarwal et al, 2018;Gangurde et al, 2020Gangurde et al, , 2021Kumar et al, 2020;Pandey et al, 2020;Shasidhar et al, 2020;Sinha et al, 2020;Jadhav et al, 2021;Soni et al, 2021;Aravind et al, 2022;Bomireddy et al, 2022;Liu et al, 2022;Patel et al, 2022). Therefore, it is vital to identify new potential genes associated with multiple stress tolerance and trait improvement in peanut for better protein-rich food supply, particularly in Asian and African countries.…”