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<p>The genetic basis of topsoil-foraging root system architecture (RSA) contrary to a steep-cheap-deep root ideotype typical of most annual crops, and how it has evolved in jute (<i>Corchorus olitorius</i>) during its domestication as a bast-fibre crop are unknown. For jute is cross-incompatible with wild <i>Corchorus</i> species, we used an F<sub>2</sub>-F<sub>2:3</sub> population founded by a <i>bast fibre-shy</i> mutant with impaired fibre development, RSA and nitrate reductase activity (NRA) and its corresponding wild-type (WT). To detect quantitative trait loci (QTL) for 11 RSA-related traits, leaf and root NRA and shoot biomass, we generated the whole-plant transcriptomes and constructed a genome-integrated genetic map comprising genic and genomic single nucleotide polymorphisms (SNPs). We identified a total of 154 QTL anchoring 107 unique SNP loci, with 140 exerting small effects. Seventy-five percent of these were identified as multi-trait QTL associated with 42 SNP loci, suggesting a well-coordinated pleiotropic control of RSA and NRA. By analyzing the mutant to WT ratios of the QTL number, additive effects and phenotypic variance explained over the 14 traits, we show that additive effects contributed to tweaking the RSA. We identified QTL with regulatory roles and reconstructed a multidimensional QTL gene interaction network governing the jute RSA characterized by a low root to shoot ratio (RSR). This study reveals gradual domestication of topsoil-foraging RSA in jute driven by coordinated action of many small-effect QTL, with an interplay of above- and below-ground NR activities modulated by key regulatory genes. This knowledge will help maintain the delicate balance of RSA and NRA during jute varietal improvement.</p>

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Topsoil-foraging root system architecture and N-use efficiency governed by small-effect quantitative trait loci (QTL) coevolved during jute (Corchorus olitorius L.) domestication

  • 期刊论文

  • 发表日期：

    2026年1月21日

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  • Pratik Satya,
  • Nur Alam Mandal,
  • Biswanath Adhikary,
  • Avrajit Chakraborty,
  • Debajeet Das,
  • Avijit Kundu,
  • Jiban Mitra,
  • Dipnarayan Saha,
  • Subhojit Datta,
  • Ajay Kumar Mahato,
  • Sabyasachi Mitra,
  • Amit Bera,
  • Chandan Sourav Kar,
  • Kishor Gaikwad,
  • Gouranga Kar,
  • Ramcharan Bhattacharya,
  • Debabrata Sarkar,
  • Nagendra Kumar Singh

摘要

The genetic basis of topsoil-foraging root system architecture (RSA) contrary to a steep-cheap-deep root ideotype typical of most annual crops, and how it has evolved in jute (Corchorus olitorius) during its domestication as a bast-fibre crop are unknown. For jute is cross-incompatible with wild Corchorus species, we used an F2-F2:3 population founded by a bast fibre-shy mutant with impaired fibre development, RSA and nitrate reductase activity (NRA) and its corresponding wild-type (WT). To detect quantitative trait loci (QTL) for 11 RSA-related traits, leaf and root NRA and shoot biomass, we generated the whole-plant transcriptomes and constructed a genome-integrated genetic map comprising genic and genomic single nucleotide polymorphisms (SNPs). We identified a total of 154 QTL anchoring 107 unique SNP loci, with 140 exerting small effects. Seventy-five percent of these were identified as multi-trait QTL associated with 42 SNP loci, suggesting a well-coordinated pleiotropic control of RSA and NRA. By analyzing the mutant to WT ratios of the QTL number, additive effects and phenotypic variance explained over the 14 traits, we show that additive effects contributed to tweaking the RSA. We identified QTL with regulatory roles and reconstructed a multidimensional QTL gene interaction network governing the jute RSA characterized by a low root to shoot ratio (RSR). This study reveals gradual domestication of topsoil-foraging RSA in jute driven by coordinated action of many small-effect QTL, with an interplay of above- and below-ground NR activities modulated by key regulatory genes. This knowledge will help maintain the delicate balance of RSA and NRA during jute varietal improvement.