Nat Biotechnol 30:174–178Īnders S, Huber W (2010) Differential expression analysis for sequence count data. This study provided insights into the genetic and molecular mechanisms of seed weight in peanut.Ībe A, Kosugi S, Yoshida K, Natsume S, Takagi H, Kanzaki H, Matsumura H, Yoshida K, Mitsuoka C, Tamiru M, Innan H, Cano L, Kamoun S, Terauchi R (2012) Genome sequencing reveals agronomically important loci in rice using MutMap. 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. In addition, the allelic diversity of qSWB06.3 was investigated in peanut germplasm accessions. The expression patterns of candidate genes related to seed weight in qSWB06.3 were investigated using quantitative real-time PCR. 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. 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.
Furthermore, differentially expressed genes (DEGs) were identified at the three seed developmental stages between the two parents of the RIL population. Among these three QTL regions, qSWB06.3 exhibited stable expression, contributing mainly to phenotypic variance across environments. 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. 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.
However, relatively little is known about the quantitative trait loci (QTLs) and candidate genes associated with seed weight in peanut. Seed weight, as an important component of seed yield, is a significant target of peanut breeding. 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 molecular mechanisms associated with seed weight in peanut.
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