Genome-Wide Association Analysis Identifies Candidate Genes Regulating Seed Number per Silique in Arabidopsis thaliana

Abstract

Seed weight and number ultimately determine seed yield. Arabidopsis seed number comprised of silique number and seed number per silique (SNS). Comparing seed development and weight, determinants of seed number remain largely uncharacterized. In this study, taking advantage of 107 available Arabidopsis accessions, genome-wide association analysis (GWAS) was employed to identify the candidate genes regulating SNS. GWAS-based genotype and phenotype association analysis identified 38 most significant SNPs marker sites that were mapped to specific chromosomal positions and allowed us to screen for dozens of candidate genes. One of them (PIN3) was selected for functional validation based on gene expression analysis. It is a positive regulator of Arabidopsis SNS. Although silique length of PIN3 loss of function mutant was not significantly changed, its SNS and seed density (SD) were significantly reduced as compared with the wild type. Notably, PIN3 overexpression lines driven by a placenta-specific promoter STK exhibited significantly shorter siliques, slightly reduced SNS, but significant increased SD compared with wild type, suggesting that PIN3 positively regulates SD through inducing ovule primordia initiation regardless of the placenta size. Ovule initiation determines the maximal possibility of SNS, and new genes and mechanism regulating SNS through modulating ovule initiation is worth further investigated.

Asynchrony of ovule primordia initiation in Arabidopsis

“…The phenotype of the crowded ovule in bzr1-1D at stage 9 indicates higher ovule density (the ratio of the ovule number to the placenta length) ( ) ( Jiang et al, 2020 ), and suggests that BR increases seed number not only through promoting placentae elongation but also through promoting ovule primordia initiation. Flowers treated with 2,4-epibrassinolide (eBL) at stage 8-9 exhibited increased DR5 signal, indicating a significantly enhanced auxin response ( Fig.…”

Effects of BrMYC2/3/4 on Plant Development, Glucosinolate Metabolism, and Sclerotinia sclerotiorum Resistance in Transgenic Arabidopsis thaliana

“…Seed size is a key agronomic trait that determines the grain yield and breeding of plants (Shirley et al, 2019). The number and weight of the seed ultimately determine seed yield (Jiang et al, 2020). In this study, we found that as a result of overexpression of each of BrMYC2/3-1/3-2/4-1/4-2, both the seed length and seed weight decreased (Figures 4C,E), while seed number per silique increased except for BrMYC2 OE as compared to Ctrl (Figure 4F).…”

“…In order to determine the seed yield, 30 T3 lines were taken from each genotype. After the siliques matured, the first five incompletely developed siliques were removed from the main inflorescence axis as described before (Jiang et al, 2020). The first intact siliques were then used to assess the number of seeds per silique.…”

PIN3 positively regulates the late initiation of ovule primordia in Arabidopsis thaliana

“…We have demonstrated that PIN3 positively regulates the seed number per silique and seed density in A. thaliana [49]. However, how PIN3 controls seed number remains unclear.…”

“…To unravel the importance of PIN3 in ovule initiation, we identified two new pin3 mutants SALK_113246 and SALK_126753 and named them as pin3-1 and pin3-2, respectively [49], which have the same names with the two reported pin3 mutants [45]. These mutants are four different alleles.…”