Yang Liu, Congyang Yi, Qian Liu, Chunhui Wang, Wenpeng Wang, Fangpu Han, Xiaojun Hu

Plants (Basel); 2022 Nov 28; 11(23):3276. doi: 10.3390/plants11233276.

Abstract

Seed size is the major yield component and a key target trait that is selected during peanut breeding. However, the mechanisms that regulate peanut seed size are unknown. Two peanut mutants with bigger seed size were isolated in this study by ⁶⁰Co treatment of a common peanut landrace, Huayu 22, and were designated as the "big seed" mutant lines (hybs). The length and weight of the seed in hybs were about 118% and 170% of those in wild-type (WT), respectively. We adopted a multi-omics approach to identify the genomic locus underlying the hybs mutants. We performed whole genome sequencing (WGS) of WT and hybs mutants and identified thousands of large-effect variants (SNPs and indels) that occurred in about four hundred genes in hybs mutants. Seeds from both WT and hybs lines were sampled 20 days after flowering (DAF) and were used for RNA-Seq analysis; the results revealed about one thousand highly differentially expressed genes (DEGs) in hybs compared to WT. Using a method that combined large-effect variants with DEGs, we identified 45 potential candidate genes that shared gene product mutations and expression level changes in hybs compared to WT. Among the genes, two candidate genes encoding cytochrome P450 superfamily protein and NAC transcription factors may be associated with the increased seed size in hybs. The present findings provide new information on the identification and functional research into candidate genes responsible for the seed size phenotype in peanut.

See https://pubmed.ncbi.nlm.nih.gov/36501316/

Figure 2

Depth−of−coverage of sequence reads from WT, hybs1, and hybs2 along the chromosomes. (A,B) Distribution of the sliding window average of depth ratio in hybs1 (A) and hybs2 (B). The window size was 100 kb. The depth ratio was calculated by dividing the depth−of−coverage of mutant by the depth−of−coverage of WT; the ratio was then log₁₀ transformed. Red: A subgenome; Skyblue: B subgenome.