Genetic mapping and QTL analysis for peanut smut resistance

Abstract

Background Peanut smut is a disease caused by the fungus Thecaphora frezii Carranza & Lindquist to which most commercial cultivars in South America are highly susceptible. It is responsible for severely decreased yield and no effective chemical treatment is available to date. However, smut resistance has been identified in wild Arachis species and further transferred to peanut elite cultivars. To identify the genome regions conferring smut resistance within a tetraploid genetic background, this study evaluated a RIL population {susceptible Arachis hypogaea subsp. hypogaea (JS17304-7-B) × resistant synthetic amphidiploid (JS1806) [A. correntina (K 11905) × A. cardenasii (KSSc 36015)] × A. batizocoi (K 9484)4×} segregating for the trait. Results A SNP based genetic map arranged into 21 linkage groups belonging to the 20 peanut chromosomes was constructed with 1819 markers, spanning a genetic distance of 2531.81 cM. Two consistent quantitative trait loci (QTLs) were identified qSmIA08 and qSmIA02/B02, located on chromosome A08 and A02/B02, respectively. The QTL qSmIA08 at 15.20 cM/5.03 Mbp explained 17.53% of the phenotypic variance, while qSmIA02/B02 at 4.0 cM/3.56 Mbp explained 9.06% of the phenotypic variance. The combined genotypic effects of both QTLs reduced smut incidence by 57% and were stable over the 3 years of evaluation. The genome regions containing the QTLs are rich in genes encoding proteins involved in plant defense, providing new insights into the genetic architecture of peanut smut resistance. Conclusions A major QTL and a minor QTL identified in this study provide new insights into the genetic architecture of peanut smut resistance that may aid in breeding new varieties resistant to peanut smut.

A first insight into the genetics of maturity trait in Runner × Virginia types peanut background

“…SNPs represent one such marker group, which constitutes an abundant source of genetic variation at the genome level, significantly improving genome coverage and marker saturation 39 . So far, much of the effort on peanut SNP-based genotyping and trait mapping was made on several agronomically important traits such as pod and seed traits 40 – 42 and disease-related traits 43 – 48 . In this study, with the application of SNP microarray technology and focused phenotyping, two stable QTL for TTM was exposed in a recombinant inbred population from a Runner × Virginia cross with the parental TTM differing by ~ 10–15 days.…”

Two QTLs govern the resistance to Sclerotinia minor in an interspecific peanut RIL population

“…The QTL mapping was carried out with the R/qtl2 package using the genetic map constructed from the same population of RILs (de Blas et al., 2021). The adjusted means of the phenotypic data (incidence) of the 103 RILs obtained from the model described in statistical analysis, were used for QTL analysis.…”

“…Deighton (Moss et al, 1981;Stalker & Wynne., 1979;Wynne & Halward., 1989), Sclerotinia blight caused by Sclerotinia minor Jagger and S. sclerotiorum (Lib.) de Bary (Isleib et al, 2006;Tallury, Hollowell, et al, 2014), root-knot nematodes caused by Meloidogyne arenaria (Neal) (Ballén et al, 2019;Simpson & Starr, 2001), and peanut smut caused by Thecaphora frezii (de Blas et al, 2019(de Blas et al, , 2021. Since early 2000s molecular markers have been used on genetic improvement in peanuts Bertioli et al, 2014;Chu et al, 2019;Pandey et al, 2014;Varshney, 2016;Varshney et al, 2006).…”

First draft genome of Thecaphora frezii, causal agent of peanut smut disease

“…For example, United States is a major exporter of peanuts [5], but it also imports peanuts from other countries [6] including Argentina [7]. Scientists from the U.S. and Argentina are working in collaboration to better understand the disease and to identify resistant peanut germplasm [8][9][10][11]. Part of that effort is to know the genetics of the pathogen.…”