Hakla Haroon Rashid, Sharma Shubham, Urfan Mohammad, Mandlik Rushil, Kumawat Surbhi, Rajput Prakriti, Khajuria Bhubneshwari, Chowdhary Rehana, Deshmukh Rupesh, Roychowdhury Rajib, Pal Sikander
Plant Physiology Laboratory, Department of Botany, University of Jammu, Jammu 180006, India.
Central Integrated Pest Management Centre (CIPMC), Srinagar 190008, India.
Plants (Basel). 2024 Feb 5;13(3):457. doi: 10.3390/plants13030457.
Phosphate (P) is a crucial macronutrient for normal plant growth and development. The P availability in soils is a limitation factor, and understanding genetic factors playing roles in plant adaptation for improving P uptake is of great biological importance. Genome-wide association studies (GWAS) have become indispensable tools in unraveling the genetic basis of complex traits in various plant species. In this study, a comprehensive GWAS was conducted on diverse tomato ( L.) accessions grown under normal and low P conditions for two weeks. Plant traits such as shoot height, primary root length, plant biomass, shoot inorganic content (SiP), and root inorganic content (RiP) were measured. Among several models of GWAS tested, the Bayesian-information and linkage disequilibrium iteratively nested keyway (BLINK) models were used for the identification of single nucleotide polymorphisms (SNPs). Among all the traits analyzed, significantly associated SNPs were recorded for PB, i.e., 1 SNP (SSL4.0CH10_49261145) under control P, SiP, i.e., 1 SNP (SSL4.0CH08_58433186) under control P and 1 SNP (SSL4.0CH08_51271168) under low P and RiP i.e., 2 SNPs (SSL4.0CH04_37267952 and SSL4.0CH09_4609062) under control P and 1 SNP (SSL4.0CH09_3930922) under low P condition. The identified SNPs served as genetic markers pinpointing regions of the tomato genome linked to P-responsive traits. The novel candidate genes associated with the identified SNPs were further analyzed for their protein-protein interactions using STRING. The study provided novel candidate genes, viz. for PB under control, , and for SiP and , , , and for RiP under low P condition. These findings offer a glimpse into the genetic diversity of tomato accessions' responses to P uptake, highlighting the potential for tailored breeding programs to develop P-efficient tomato varieties that could adapt to varying soil conditions, making them crucial for sustainable agriculture and addressing global challenges, such as soil depletion and food security.
磷（P）是植物正常生长发育所必需的大量营养素。土壤中磷的有效性是一个限制因素，了解植物适应过程中参与提高磷吸收的遗传因素具有重要的生物学意义。全基因组关联研究（GWAS）已成为揭示各种植物物种复杂性状遗传基础不可或缺的工具。在本研究中，对在正常磷和低磷条件下生长两周的不同番茄（L.）种质进行了全面的GWAS。测量了株高、初生根长度、植物生物量、地上部无机磷含量（SiP）和根部无机磷含量（RiP）等植物性状。在测试的几种GWAS模型中，贝叶斯信息和连锁不平衡迭代嵌套键路（BLINK）模型用于鉴定单核苷酸多态性（SNP）。在所有分析的性状中，记录到与磷含量（PB）显著相关的SNP，即在正常磷条件下有1个SNP（SSL4.0CH10_49261145），与地上部无机磷含量（SiP）相关的SNP，即在正常磷条件下有1个SNP（SSL4.0CH08_58433186），在低磷条件下有1个SNP（SSL4.0CH08_51271168），与根部无机磷含量（RiP）相关的SNP，即在正常磷条件下有2个SNP（SSL4.0CH04_37267952和SSL4.0CH09_4609062），在低磷条件下有1个SNP（SSL4.0CH09_3930922）。所鉴定的SNP作为遗传标记，确定了番茄基因组中与磷响应性状相关的区域。使用STRING进一步分析了与所鉴定SNP相关的新候选基因的蛋白质-蛋白质相互作用。该研究提供了新的候选基因，即在正常条件下与磷含量（PB）相关的基因，与地上部无机磷含量（SiP）相关的基因，以及在低磷条件下与根部无机磷含量（RiP）相关的基因。这些发现揭示了番茄种质对磷吸收反应的遗传多样性，突出了定制育种计划开发能适应不同土壤条件的磷高效番茄品种的潜力，这对于可持续农业和应对土壤贫瘠及粮食安全等全球挑战至关重要。
