Genome-Wide Association Analysis for Phosphorus Use Efficiency Traits in Mungbean (Vigna radiata L. Wilczek) Using Genotyping by Sequencing Approach

Frontiers in Plant Science

卷:11

Akanksha Singh¹  Shiv Kumar²  Surendra Kumar Meena³  Tilak Raj Sharma⁴  Venkata Ravi Prakash Reddy⁵  Shouvik Das⁵  Gyan Prakash Mishra⁵  Harsh Kumar Dikshit⁵  Priti⁵  Muraleedhar Aski⁵  Twinkle Kumari Bhagat⁵  Padmavati Ganpat Gore⁶  Kuldeep Tripathi⁷  Renu Pandey⁸  Madan Pal Singh⁸  Ramakrishnan Nair⁹ 

[1] Amity Institute of Organic Agriculture, Amity University, Noida, India;

[2] Biodiversity and Integrated Gene Management Program, International Center for Agricultural Research in the Dry Areas, Rabat, Morocco;

[3] Division of Basic Science, ICAR-Indian Institute of Pulses Research, Kanpur, India;

[4] Division of Crop Science, Indian Council of Agricultural Research, New Delhi, India;

[5] Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India;

[6] Division of Germplasm Conservation, ICAR-National Bureau of Plant Genetic Resources, New Delhi, India;

[7] Division of Germplasm Evaluation, ICAR-National Bureau of Plant Genetic Resources, New Delhi, India;

[8] Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, India;

[9] South and Central Asia, World Vegetable Center, Patancheru, India;

关键词: mungbean;    PUE traits;    GBS;    GWAS;    candidate genes;   

DOI  :  10.3389/fpls.2020.537766

来源: DOAJ

【 摘 要 】

Mungbean (Vigna radiata L. Wilczek) is an annual grain legume crop affected by low availability of phosphorus. Phosphorus deficiency mainly affects the growth and development of plants along with changes in root morphology and increase in root-to-shoot ratio. Deciphering the genetic basis of phosphorus use efficiency (PUE) traits can benefit our understanding of mungbean tolerance to low-phosphorus condition. To address this issue, 144 diverse mungbean genotypes were evaluated for 12 PUE traits under hydroponics with optimum- and low-phosphorus levels. The broad sense heritability of traits ranged from 0.63 to 0.92 and 0.58 to 0.92 under optimum- and low-phosphorus conditions, respectively. This study, reports for the first time such a large number of genome wide Single nucleotide polymorphisms (SNPs) (76,160) in mungbean. Further, genome wide association study was conducted using 55,634 SNPs obtained by genotyping-by-sequencing method. The results indicated that total 136 SNPs shared by both GLM and MLM models were associated with tested PUE traits under different phosphorus regimes. We have identified SNPs with highest p value (–log10(p)) for some traits like, TLA and RDW with p value (–log10(p)) of more than 6.0 at LP/OP and OP condition. We have identified nine SNPs (three for TLA and six for RDW trait) which was found to be present in chromosomes 8, 4, and 7. One SNP present in Vradi07g06230 gene contains zinc finger CCCH domain. In total, 71 protein coding genes were identified, of which 13 genes were found to be putative candidate genes controlling PUE by regulating nutrient uptake and root architectural development pathways in mungbean. Moreover, we identified three potential candidate genes VRADI11G08340, VRADI01G05520, and VRADI04G10750 with missense SNPs in coding sequence region, which results in significant variation in protein structure at tertiary level. The identified SNPs and candidate genes provide the essential information for genetic studies and marker-assisted breeding program for improving low-phosphorus tolerance in mungbean.

【 授权许可】

Unknown