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Background: Pod shell thickness (PST) is an important agronomic trait of peanut because it affects the ability of shells to resist pest infestations and pathogen attacks, while also influencing the peanut shelling process. However, very few studies have explored the genetic basis of PST. Results: An F2 segregating population derived from a cross between the thick-shelled cultivar Yueyou 18 (YY18) and the thin-shelled cultivar Weihua 8 (WH8) was used to identify the quantitative trait loci (QTLs) for PST. On the basis of a bulked segregant analysis sequencing (BSA-seq), four QTLs were preliminarily mapped to chromosomes 3, 8, 13, and 18. Using the genome resequencing data of YY18 and WH8, 22 kompetitive allele-specific PCR (KASP) markers were designed for the genotyping of the F2 population. Two major QTLs (qPSTA08 and qPSTA18) were identified and finely mapped, with qPSTA08 detected on chromosome 8 (0.69-Mb physical genomic region) and qPSTA18 detected on chromosome 18 (0.15-Mb physical genomic region). Moreover, qPSTA08 and qPSTA18 explained 31.1–32.3% and 16.7–16.8% of the phenotypic variation, respectively. Fifteen genes were detected in the two candidate regions, including three genes with nonsynonymous mutations in the exon region. Two molecular markers (Tif2_A08_31713024 and Tif2_A18_7198124) that were developed for the two major QTL regions effectively distinguished between thick-shelled and thin-shelled materials. Subsequently, the two markers were validated in four F2:3 lines selected. Conclusions: The QTLs identified and molecular markers developed in this study may lay the foundation for breeding cultivars with a shell thickness suitable for mechanized peanut shelling. [ABSTRACT FROM AUTHOR]

Key message: QTLs for growth habit are identified on Arahy.15 and Arahy.06 in peanut, and diagnostic markers are developed and validated for further use in marker-assisted breeding. Peanut is a unique legume crop because its pods develop and mature underground. The pegs derive from flowers following pollination, then reach the ground and develop into pods in the soil. Pod number per plant is influenced by peanut growth habit (GH) that has been categorized into four types, including erect, bunch, spreading and prostrate. Restricting pod development at the plant base, as would be the case for peanut plants with upright lateral branches, would decrease pod yield. On the other hand, GH characterized by spreading lateral branches on the ground would facilitate pod formation on the nodes, thereby increasing yield potential. We describe herein an investigation into the GH traits of 521 peanut recombinant inbred lines grown in three distinct environments. Quantitative trait loci (QTLs) for GH were identified on linkage group (LG) 15 between 203.1 and 204.2 cM and on LG 16 from 139.1 to 139.3 cM. Analysis of resequencing data in the identified QTL regions revealed that single nucleotide polymorphism (SNP) or insertion and/or deletion (INDEL) at Arahy15.156854742, Arahy15.156931574, Arahy15.156976352 and Arahy06.111973258 may affect the functions of their respective candidate genes, Arahy.QV02Z8, Arahy.509QUQ, Arahy.ATH5WE and Arahy.SC7TJM. These SNPs and INDELs in relation to peanut GH were further developed for KASP genotyping and tested on a panel of 77 peanut accessions with distinct GH features. This study validates four diagnostic markers that may be used to distinguish erect/bunch peanuts from spreading/prostrate peanuts, thereby facilitating marker-assisted selection for GH traits in peanut breeding. [ABSTRACT FROM AUTHOR]