A genome-wide association study reveals a novel regulator of ovule number and fertility in Arabidopsis thaliana

Yuan, Jing; Kessler, Sharon A

doi:10.1371/journal.pgen.1007934

Cited by 42 publications

(37 citation statements)

References 59 publications

(75 reference statements)

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“…Overexpression of genes regulating fertility and seed set does not increase SNS because they do not enhance the ovule initiation and ovule number. Although GWAS analysis of ovule number identified NERD, which positively regulates ovule number and SNS, it still regulated ovule number through helping ovule development and fertility [60]. However, only a few genes were reported to positively regulate SNS mainly through increasing ovule number by elongating placenta size [16].…”

Section: Discussionmentioning

confidence: 99%

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

Jiang¹,

Hong²,

Jiang³

et al. 2020

Plants

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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.

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Section: Discussionmentioning

confidence: 99%

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

Jiang¹,

Hong²,

Jiang³

et al. 2020

Plants

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“…Protein sequence alignment analysis showed that PL1 shared high identities with the homologs identified, not only from primarily monocots and dicots but also from distantly related gymnosperms and cryptogams ( Figure 4G and Figure S9 and Table S4). Protein sequence alignment and phylogenetic analysis also showed that NEW ENHANCER of ROOT DWARFISM 1 (NERD1), an integrin-α N-terminal domain containing protein required for Arabidopsis reproductive development [56,57], is an orthologue of PL1 ( Figure 4G and Figure S9), suggesting a functional conservation between these two proteins. Overall, these results suggested that PL1 is a member of a highly conserved protein family in terrestrial plants.…”

Section: Pl1 Encodes a Conserved Integrin-α Fg-gap Repeat-containing mentioning

confidence: 97%

A Silent Exonic Mutation in a Rice Integrin-α FG-GAP Repeat-Containing Gene Causes Male-Sterility by Affecting mRNA Splicing

Zou

Zhou

et al. 2020

IJMS

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Pollen development plays crucial roles in the life cycle of higher plants. Here we characterized a rice mutant with complete male-sterile phenotype, pollen-less 1 (pl1). pl1 exhibited smaller anthers with arrested pollen development, absent Ubisch bodies, necrosis-like tapetal hypertrophy, and smooth anther cuticular surface. Molecular mapping revealed a synonymous mutation in the fourth exon of PL1 co-segregated with the mutant phenotype. This mutation disrupts the exon-intron splice junction in PL1, generating aberrant mRNA species and truncated proteins. PL1 is highly expressed in the tapetal cells of developing anther, and its protein is co-localized with plasma membrane (PM) and endoplasmic reticulum (ER) signal. PL1 encodes an integrin-α FG-GAP repeat-containing protein, which has seven β-sheets and putative Ca2+-binding motifs and is broadly conserved in terrestrial plants. Our findings therefore provide insights into both the role of integrin-α FG-GAP repeat-containing protein in rice male fertility and the influence of exonic mutation on intronic splice donor site selection.

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“…These chickpea gametophyte QTL had significant effects on sporophyte female fitness, not because the faster gametophytes are generally superior but because the gene is expressed in both pollen and seed pods. Similarly, a major regulator of ovule number, a sporophyte trait identified in a GWAS among A. thaliana accessions, exhibited significant overlap with male gametophyte development loci ( Yuan and Kessler, 2019 ). Evidence for pleiotropy between vegetative and reproductive tissue also appears outside of the seed plants.…”

Section: Does Gametophytic Selection Have Positive Negative or Neutmentioning

confidence: 99%

Evolutionary Genomics of Plant Gametophytic Selection

Beaudry

Rifkin

Barrett

et al. 2020

Plant Communications

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It has long been recognized that natural selection during the haploid gametophytic phase of the plant life cycle may have widespread importance for rates of evolution and the maintenance of genetic variation. Recent theoretical advances have further highlighted the significance of gametophytic selection for diverse evolutionary processes. Genomic approaches offer exciting opportunities to address key questions about the extent and effects of gametophytic selection on plant evolution and adaptation. Here, we review the progress and prospects for integrating functional and evolutionary genomics to test theoretical predictions, and to examine the importance of gametophytic selection on genetic diversity and rates of evolution. There is growing evidence that selection during the gametophyte phase of the plant life cycle has important effects on both gene and genome evolution and is likely to have important pleiotropic effects on the sporophyte. We discuss the opportunities to integrate comparative population genomics, genome-wide association studies, and experimental approaches to further distinguish how differential selection in the two phases of the plant life cycle contributes to genetic diversity and adaptive evolution.

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A genome-wide association study reveals a novel regulator of ovule number and fertility in Arabidopsis thaliana

Cited by 42 publications

References 59 publications

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

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

A Silent Exonic Mutation in a Rice Integrin-α FG-GAP Repeat-Containing Gene Causes Male-Sterility by Affecting mRNA Splicing

Evolutionary Genomics of Plant Gametophytic Selection

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