Whole‐genome sequencing based discovery of candidate genes and diagnostic markers for seed weight in groundnut

Abstract

Seed weight in groundnut (Arachis hypogaea L.) has direct impact on yield as well as market price because of preference for bold seeds by consumers and industry, thereby making seed‐size improvement as one of the most important objectives of groundnut breeding programs globally. Marker‐based early generation selection can accelerate the process of breeding for developing large‐seeded varieties. In this context, we deployed the quantitative trait locus‐sequencing (QTL‐seq) approach on a biparental mapping population (Chico × ICGV 02251) to identify candidate genes and develop markers for seed weight in groundnut. A total of 289.4–389.4 million reads sequencing data were generated from three libraries (ICGV 02251 and two extreme bulks) achieving 93.9–95.1% genome coverage and 8.34–9.29× average read depth. The analysis of sequencing data using QTL‐seq pipeline identified five genomic regions (three on chromosome B06 and one each on chromosomes B08 and B09) for seed weight. Detailed analysis of above associated genomic regions detected 182 single‐nucleotide polymorphisms (SNPs) in genic and intergenic regions, and 11 of these SNPs were nonsynonymous in the genomic regions of 10 candidate genes including Ulp proteases and BIG SEED locus genes. Kompetitive allele specific polymerase chain reaction (KASP) markers for 14 SNPs were developed, and four of these markers (snpAH0031, snpAH0033, snpAH0037, and snpAH0038) were successfully validated for deployment in breeding for large‐seeded groundnut varieties.

PSW1, an LRR receptor kinase, regulates pod size in peanut

“…Peanut pod size is an important yield trait and shows wide variation across accessions. Based on trait heritability and correlation analysis, PL is positively correlated with SL, seed weight, and pod weight, making PL an important yield-related indicator (Khan et al, 2022). The identified pod/seed size and weight-related QTLs were mainly concentrated on chromosomes 05, 07, 08 and 09 in peanut (Alyr et al, 2020;Chavarro et al, 2020;Fonceka et al, 2012;Gangurde et al, 2020Gangurde et al, , 2022Gomez Selvaraj et al, 2009;Zhang et al, 2019), however, few defined pod size related genes and regulatory mechanisms have been characterized.…”

“…Based on trait heritability and correlation analysis, PL is positively correlated with SL, seed weight, and pod weight, making PL an important yield‐related indicator (Khan et al ., 2022). The identified pod/seed size and weight‐related QTLs were mainly concentrated on chromosomes 05, 07, 08 and 09 in peanut (Alyr et al ., 2020; Chavarro et al ., 2020; Fonceka et al ., 2012; Gangurde et al ., 2020, 2022; Gomez Selvaraj et al ., 2009; Zhang et al ., 2019), however, few defined pod size related genes and regulatory mechanisms have been characterized. Here, we identify a QTL related to pod size in peanut through genetic mapping using a segregating population derived from a cross between two peanut cultivars (ND_S and ND_L) with extreme differences in pod size/weight (Figure S1).…”

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

“…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).…”

Silicon Application for the Modulation of Rhizosphere Soil Bacterial Community Structures and Metabolite Profiles in Peanut under Ralstonia solanacearum Inoculation

“…Cultivated peanut ( Arachis hypogaea L.) is one of the most important leguminous oilseeds and food crops used for high-quality eatable oil and protein [ 1 ]. To date, ~54 million tons of peanuts are produced annually around the world [ 2 , 3 ], but peanut bacterial wilt (PBW) a soil-borne vascular disease caused by Ralstonia solanacearum , severely damages worldwide peanut production due to its widespread distribution and high pathogenicity [ 4 , 5 , 6 ]. Particularly, PBW causes ~100% yield loss under severe disease infestation [ 7 ].…”