Detection of a major QTL and development of KASP markers for seed weight by combining QTL-seq, QTL-mapping and RNA-seq in peanut.

Yuning Chen,Xin Wang,Yong Lei,Kede Liu,Boshou Liao,Zhihui Wang,Liying Yan,Huifang Jiang,Yanping Kang,Dongxin Huai

doi:10.1007/s00122-022-04069-0

Abstract

Combining QTL-seq, QTL-mapping and RNA-seq identified a major QTL and candidate genes, which contributed to the development of KASP markers and understanding of molecularmechanisms associated with seed weight in peanut. Seed weight, as an important component of seed yield, is a significant target of peanut breeding. However, relatively little is known about the quantitative trait loci (QTLs) and candidate genes associated with seed weight in peanut. In this study, three major QTLs on chromosomes A05, B02, and B06 were determined by applying the QTL-seq approach in a recombinant inbred line (RIL) population. Based on conventional QTL-mapping, these three QTL regions were successfully narrowed down through newly developed single nucleotide polymorphism (SNP) and simple sequence repeat markers. Among these three QTL regions, qSWB06.3 exhibited stable expression, contributing mainly to phenotypic variance across environments. Furthermore, differentially expressed genes (DEGs) were identified at the three seed developmental stages between the two parents of the RIL population. It was found that the DEGs were widely distributed in the ubiquitin-proteasome pathway, the serine/threonine-protein pathway, signal transduction of hormones and transcription factors. Notably, DEGs at the early stage were mostly involved in regulating cell division, whereas DEGs at the middle and late stages were primarily involved in cell expansion during seed development. The expression patterns of candidate genes related to seed weight in qSWB06.3 were investigated using quantitative real-time PCR. In addition, the allelic diversity of qSWB06.3 was investigated in peanut germplasm accessions. The marker Ah011475 has higher efficiency for discriminating accessions with different seed weights, and it would be useful as a diagnostic marker in marker-assisted breeding. This study provided insights into the genetic and molecularmechanisms of seed weight in peanut.

Highlights

Peanut (Arachis hypogaea L.) is an important oilseed crop that is widely planted in more than 100 countries
We successfully identified the candidate major QTLs associated with seed weight using next generation sequencing (NGS)-based QTL-seq approach
Among these candidate QTLs, three of them were further validated and narrowed down by single nucleotide polymorphisms (SNPs) and SSR marker-based traditional QTL mapping. These results indicated that QTL-seq is a quick and efficient method, which can be used to scan and identify major QTLs at a genome-wide scale in peanut

Summary

Introduction

Peanut (Arachis hypogaea L.) is an important oilseed crop that is widely planted in more than 100 countries. It provides high-quality edible oil and protein for humans in the semi-arid tropics. It is crucial to increase the world-wide peanut production to fulfill the dietary demand of an increasing global population. Seed weight is considered as a crucial seed trait and generally positively correlated with yield as well as oil and protein contents (Shirasawa et al, 2012b; Chen et al, 2016a; Chen et al, 2017). Identification of QTLs controlling seed weight and characterization of the underlying candidate genes will benefit molecular breeding and yield enhancement of peanut

Methods

Results

Conclusion