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Key message <p>A paralog of <i>Cell Size Regulator</i> (<i>CSR</i>), <i>CSR-like1</i>, underlies the novel <i>fw6.2</i> QTL in tomato. The gene and locus regulate fruit weight by increasing pericarp cell size and its function on fruit weight appears to be conserved in other crops.</p> Abstract <p>Fruit weight is a quantitative trait that was under strong selection during the domestication of fruit and vegetable crops such as tomato (<i>Solanum lycopersicum</i>). While numerous fruit weight QTLs have been identified, only three tomato fruit weight genes have been cloned. In this study, we utilized a genetically diverse tomato panel, the Varitome collection, to identify additional genetic loci that control fruit weight. We mapped and fine mapped two fruit weight QTLs on chromosome 6, <i>fw6.1</i> and <i>fw6.2</i>, by using Genome Wide Association studies (GWAS) and linkage mapping in bi-parental populations. We identified a member of the <i>Cell Size Regulator</i> family, <i>CSR-like1</i>, as the likely candidate underlying <i>fw6.2</i>. The near isogenic lines (NILs) carrying the derived allele of <i>fw6.2</i> produced heavier fruits with larger fruit pericarp cells than lines with wildtype (WT) allele. Transgenic downregulation of <i>CSR-like1</i> led to a decrease in fruit weight and pericarp cells, supporting the role of this gene at the <i>fw6.2</i> locus. The haplotype analysis implied that the <i>CSR-like1</i>-Derived (<i>CSR-like1</i>-D) allele was selected in the transition from the fully wild <i>S. pimpinellifolium</i> to the earliest <i>S. lycopersicum cerasiforme</i> accessions<i>.</i> Four single nucleotide polymorphisms (SNPs) were identified in the regulatory region of <i>CSR-like1</i> that were conserved in the accessions carrying <i>CSR-like1</i>-WT and were significantly associated with lower fruit weight and pericarp cell size at the locus. Moreover, a pepper GWAS identified a <i>CSR-like1</i> ortholog that was associated with fruit weight. Together, our findings established <i>CSR-like1</i> as a novel fruit weight gene likely conserved in other crops in the Solanaceae family.</p>

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Fruit weight regulation by a paralog of Cell Size Regulator (CSR) in tomato and other crops

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2026年3月5日

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  • Qian Feng,
  • Lara Pereira,
  • Manoj Sapkota,
  • Krishna Sai Karnatam,
  • Yanbing Wang,
  • Padma Nimmakayala,
  • Umesh K. Reddy,
  • Esther van der Knaap

摘要

Key message

A paralog of Cell Size Regulator (CSR), CSR-like1, underlies the novel fw6.2 QTL in tomato. The gene and locus regulate fruit weight by increasing pericarp cell size and its function on fruit weight appears to be conserved in other crops.

Abstract

Fruit weight is a quantitative trait that was under strong selection during the domestication of fruit and vegetable crops such as tomato (Solanum lycopersicum). While numerous fruit weight QTLs have been identified, only three tomato fruit weight genes have been cloned. In this study, we utilized a genetically diverse tomato panel, the Varitome collection, to identify additional genetic loci that control fruit weight. We mapped and fine mapped two fruit weight QTLs on chromosome 6, fw6.1 and fw6.2, by using Genome Wide Association studies (GWAS) and linkage mapping in bi-parental populations. We identified a member of the Cell Size Regulator family, CSR-like1, as the likely candidate underlying fw6.2. The near isogenic lines (NILs) carrying the derived allele of fw6.2 produced heavier fruits with larger fruit pericarp cells than lines with wildtype (WT) allele. Transgenic downregulation of CSR-like1 led to a decrease in fruit weight and pericarp cells, supporting the role of this gene at the fw6.2 locus. The haplotype analysis implied that the CSR-like1-Derived (CSR-like1-D) allele was selected in the transition from the fully wild S. pimpinellifolium to the earliest S. lycopersicum cerasiforme accessions. Four single nucleotide polymorphisms (SNPs) were identified in the regulatory region of CSR-like1 that were conserved in the accessions carrying CSR-like1-WT and were significantly associated with lower fruit weight and pericarp cell size at the locus. Moreover, a pepper GWAS identified a CSR-like1 ortholog that was associated with fruit weight. Together, our findings established CSR-like1 as a novel fruit weight gene likely conserved in other crops in the Solanaceae family.