Discovery of Major Quantitative Trait Loci and Candidate Genes for Fresh Seed Dormancy in Groundnut

Abstract

Spanish bunch groundnut varieties occupy most of the cultivated area in Asia and Africa, and these varieties lack required 2-3 weeks of fresh seed dormancy (FSD) hampering kernel quality. Genomic breeding can help to improve commercial groundnut cultivars for FSD in a shorter time with greater precision. In this regard, a recombinant inbred line (RIL) population from the cross ICGV 02266 (non-dormant) × ICGV 97045 (dormant) was developed and genotyped with a 5 K mid-density genotyping assay. A linkage map was constructed with 325 SNP loci spanning a total map length of 2335.3 cM and five major QTLs were identified on chromosomes Ah01, Ah11, Ah06, Ah16 and Ah17. Based on differential gene expression using transcriptomic information from dormant (Tifrunner) and non-dormant (ICGV 91114) genotypes, histone deacetylases, histone-lysine N-methyltransferase, cytochrome P450, protein kinases, and ethylene-responsive transcription factor were identified as key regulators involved in the hormonal regulation of dormancy. Six Kompetitive Allele Specific PCR (KASP) markers were successfully validated in the diverse panel including selected RILs of the same population and germplasm lines. These validated KASP markers could facilitate faster breeding of new varieties with desired dormancy using marker-assisted early generation selection.

Genetic mapping identified major main‐effect and three co‐localized quantitative trait loci controlling high iron and zinc content in groundnut

“…SNP arrays offer a fast and efficient method for high‐throughput genotyping, which can be used for association analysis, diversity analysis, and QTL mapping. In groundnut, high‐density array and mid‐density SNP assays have been developed and employed in the genetic dissection of complex traits (Bomireddy et al., 2022). In this study, we constructed a genetic linkage map consisting of 474 loci, covering a map length of 1536.33 cM with an average inter‐marker distance of 2.83 cM per locus.…”

“…High‐to‐mid‐density genotyping arrays/assays are important for constructing genetic maps, identifying the genomic regions and candidate genes through genetic mapping and genome‐wide association studies (GWAS), and developing diagnostic markers for breeding programs. In groundnut, trait‐associated single‐nucleotide polymorphism (SNP) markers have been developed and validated for many traits, such as fresh seed dormancy (Bomireddy et al., 2022; Kumar et al., 2020), foliar disease resistance (Pandey et al., 2017), high oleic acid (Chu et al., 2009), seed size (Gangurde et al., 2023; Zhuang et al., 2019), leaf spot and tomato spotted wilt virus resistance (Agarwal et al., 2018, 2019), shelling percentage (Luo et al., 2019a), and bacterial wilt resistance (Luo et al., 2019b).…”

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.…”

Genome-wide identification of germin-like proteins in peanut (Arachis hypogea L.) and expression analysis under different abiotic stresses

“…Peanut is now a resource-rich legume crop with massive transcriptome data ( Clevenger et al., 2016 ; Sinha et al., 2020 ; Gangurde et al., 2021 ). Trait dissection and candidate gene discovery with linkage and association mapping attempted for several traits, for instance, yield traits ( Gangurde et al., 2020 ; Pandey et al., 2020 ; Jadhav et al., 2021 ), fresh seed dormancy ( Gangurde et al., 2020 ; Kumar et al., 2020 ; Bomireddy et al., 2022 ), disease resistance ( Dodia et al., 2019 ; Shasidhar et al., 2020 ), and aflatoxin contamination ( Pandey et al., 2019 ; Khan et al., 2020 ; Soni et al., 2020 ). The utilization of the available resources with new data is essential.…”