Elucidating SNP-based genetic diversity and population structure of advanced breeding lines of bread wheat (Triticum aestivum L.)

PeerJ

Arun Kumar Joshi¹  Uttam Kumar¹  Vipin Tomar¹  Budhi Sagar Tiwari²  Guriqbal Singh Dhillon³  Jesse Poland⁴  Ravi Prakash Singh⁵  Daljit Singh⁶ 

[1] Borlaug Institute for South Asia, New Delhi, Delhi, India;Department of Biological Sciences and Biotechnology, Institute of Advanced Research, Gandhinagar, Gandhinagar, Gujarat, India;Department of Biotechnology, Thapar Institute of Engineering and Technology, Patiala, Punjab, India;Department of Plant Pathology, Kansas State University, Manhattan, KS, United States of America;Global Wheat Program, International Maize and Wheat Improvement Centre, Texcoco, Mexico;The Climate Corporation, Bayer Crop Science, Creve Coeur, MO, USA;

关键词: Wheat;    Genotyping-by-sequencing (GBS);    SNP;    Genetic diversity;    Population structure;    Analysis of molecular variance (AMOVA);   

DOI  :  10.7717/peerj.11593

来源: DOAJ

【 摘 要 】

Genetic diversity and population structure information are crucial for enhancing traits of interest and the development of superlative varieties for commercialization. The present study elucidated the population structure and genetic diversity of 141 advanced wheat breeding lines using single nucleotide polymorphism markers. A total of 14,563 high-quality identified genotyping-by-sequencing (GBS) markers were distributed covering 13.9 GB wheat genome, with a minimum of 1,026 SNPs on the homoeologous group four and a maximum of 2,838 SNPs on group seven. The average minor allele frequency was found 0.233, although the average polymorphism information content (PIC) and heterozygosity were 0.201 and 0.015, respectively. Principal component analyses (PCA) and population structure identified two major groups (sub-populations) based on SNPs information. The results indicated a substantial gene flow/exchange with many migrants (Nm = 86.428) and a considerable genetic diversity (number of different alleles, Na = 1.977; the number of effective alleles, Ne = 1.519; and Shannon’s information index, I = 0.477) within the population, illustrating a good source for wheat improvement. The average PIC of 0.201 demonstrates moderate genetic diversity of the present evaluated advanced breeding panel. Analysis of molecular variance (AMOVA) detected 1% and 99% variance between and within subgroups. It is indicative of excessive gene traffic (less genetic differentiation) among the populations. These conclusions deliver important information with the potential to contribute new beneficial alleles using genome-wide association studies (GWAS) and marker-assisted selection to enhance genetic gain in South Asian wheat breeding programs.

【 授权许可】

Unknown