Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
, 47 (1), 293-306

Characterization of Genetic Diversity and Population Structure in Wheat Using Array Based SNP Markers

Affiliations

Characterization of Genetic Diversity and Population Structure in Wheat Using Array Based SNP Markers

Deepender Kumar et al. Mol Biol Rep.

Abstract

Genetic diversity is crucial for successful adaptation and sustained improvement in crops. India is bestowed with diverse agro-climatic conditions which makes it rich in wheat germplasm adapted to various niches. Germplasm repository consists of local landraces, trait specific genetic stocks including introgressions from wild relatives, exotic collections, released varieties, and improved germplasm. Characterization of genetic diversity is done using morpho-physiological characters as well as by analyzing variations at DNA level. However, there are not many reports on array based high throughput SNP markers having characteristics of genome wide coverage employed in Indian spring wheat germplasm. Amongst wheat SNP arrays, 35K Axiom Wheat Breeder's Array has the highest SNP polymorphism efficiency suitable for genetic mapping and genetic diversity characterization. Therefore, genotyping was done using 35K in 483 wheat genotypes resulting in 14,650 quality filtered SNPs, that were distributed across the B (~ 50%), A (~ 39%), and D (~ 10%) genomes. The total genetic distance coverage was 4477.85 cM with 3.27 SNP/cM and 0.49 cM/SNP as average marker density and average inter-marker distance, respectively. The PIC ranged from 0.09 to 0.38 with an average of 0.29 across genomes. Population structure and Principal Coordinate Analysis resulted in two subpopulations (SP1 and SP2). The analysis of molecular variance revealed the genetic variation of 2% among and 98% within subpopulations indicating high gene flow between SP1 and SP2. The subpopulation SP2 showed high level of genetic diversity based on genetic diversity indices viz. Shannon's information index (I) = 0.648, expected heterozygosity (He) = 0.456 and unbiased expected heterozygosity (uHe) = 0.456. To the best of our knowledge, this study is the first to include the largest set of Indian wheat genotypes studied exclusively for genetic diversity. These findings may serve as a potential source for the identification of uncharacterized QTL/gene using genome wide association studies and marker assisted selection in wheat breeding programs.

Keywords: 35K; AMOVA; Genetic diversity; Indian Spring wheat; Population structure; Single nucleotide polymorphism.

Similar articles

See all similar articles

References

    1. Genet Res Int. 2015;2015:431487 - PubMed

References

    1. BMC Proc. 2009 Dec 15;3 Suppl 7:S41 - PubMed

References

    1. Genetics. 2006 Feb;172(2):1165-77 - PubMed

References

    1. Front Plant Sci. 2018 Feb 06;9:104 - PubMed

References

    1. Theor Appl Genet. 2014 Feb;127(2):261-71 - PubMed

References

    1. Plant Biotechnol J. 2013 Apr;11(3):279-95 - PubMed

References

    1. BMC Bioinformatics. 2012 Sep 03;13:219 - PubMed

References

    1. BMC Bioinformatics. 2017 Mar 24;18(1):192 - PubMed

References

    1. Proc Natl Acad Sci U S A. 2013 May 14;110(20):8057-62 - PubMed

References

    1. Theor Appl Genet. 2008 Feb;116(3):439-53 - PubMed

References

    1. Bioinformatics. 2012 Oct 1;28(19):2537-9 - PubMed

References

    1. Bioinformatics. 2005 May 1;21(9):2128-9 - PubMed

References

    1. Sci Rep. 2015 Dec 03;5:17512 - PubMed

References

    1. Mol Plant. 2017 Feb 13;10(2):309-322 - PubMed

References

    1. Am J Hum Genet. 1980 May;32(3):314-31 - PubMed

References

    1. Theor Appl Genet. 2013 Jun;126(6):1477-86 - PubMed

References

    1. Proc Natl Acad Sci U S A. 1973 Dec;70(12):3321-3 - PubMed

References

    1. Proc Natl Acad Sci U S A. 1984 Dec;81(24):8014-8 - PubMed

References

    1. Biology (Basel). 2012 Aug 27;1(2):370-82 - PubMed

References

    1. Nature. 2008 Dec 11;456(7223):720-3 - PubMed

References

    1. Genetics. 1978 Jul;89(3):583-90 - PubMed

References

    1. Theor Popul Biol. 2000 May;57(3):265-71 - PubMed

References

    1. DNA Res. 2002 Aug 31;9(4):117-21 - PubMed

References

    1. Front Plant Sci. 2017 Aug 29;8:1293 - PubMed

References

    1. Plant Biotechnol J. 2012 Aug;10(6):733-42 - PubMed

References

    1. Plant J. 2016 Apr;86(1):62-74 - PubMed

References

    1. Bioinformatics. 2007 Oct 1;23(19):2633-5 - PubMed

References

    1. Genome. 2003 Jun;46(3):431-7 - PubMed

References

    1. Front Plant Sci. 2019 Apr 25;10:527 - PubMed

References

    1. BMC Genomics. 2014 May 28;15:408 - PubMed

References

    1. BMC Genomics. 2018 Aug 6;19(1):591 - PubMed

References

    1. Mol Plant. 2014 Mar;7(3):541-53 - PubMed

References

    1. Plant Biotechnol J. 2011 Dec;9(9):1086-99 - PubMed

References

    1. PLoS Biol. 2010 Mar 09;8(3):e1000326 - PubMed

References

    1. Plant Biotechnol J. 2009 May;7(4):375-90 - PubMed

References

    1. Genome Res. 2009 Sep;19(9):1639-45 - PubMed

References

    1. Genetics. 1992 Jun;131(2):479-91 - PubMed

References

    1. Science. 2018 Aug 17;361(6403): - PubMed

References

    1. Plant Biotechnol J. 2017 Mar;15(3):390-401 - PubMed

References

    1. BMC Plant Biol. 2014 Nov 29;14:320 - PubMed

References

    1. Curr Opin Plant Biol. 2002 Apr;5(2):107-11 - PubMed

References

    1. Plant Biotechnol J. 2016 May;14(5):1195-206 - PubMed

References

    1. Front Genet. 2018 Mar 12;9:76 - PubMed

References

    1. BMC Plant Biol. 2016 Jan 27;16 Suppl 1:6 - PubMed

References

    1. Front Plant Sci. 2019 Feb 20;10:184 - PubMed

References

    1. AoB Plants. 2015 Jul 17;7: - PubMed

References

    1. Front Plant Sci. 2017 Jul 18;8:1277 - PubMed

References

    1. Am J Hum Genet. 2007 Sep;81(3):559-75 - PubMed

References

    1. BMC Genomics. 2010 Dec 14;11:702 - PubMed

References

    1. PLoS One. 2014 Apr 09;9(4):e94000 - PubMed

References

    1. PLoS One. 2013 Jun 19;8(6):e66428 - PubMed

References

    1. Theor Appl Genet. 2016 Oct;129(10):1887-99 - PubMed

References

    1. Heredity (Edinb). 1999 Feb;82 ( Pt 2):117-25 - PubMed

References

    1. Genetics. 2000 Jun;155(2):945-59 - PubMed

References

    1. C R Biol. 2016 Jan;339(1):1-9 - PubMed

References

    1. PLoS One. 2018 Jan 2;13(1):e0186329 - PubMed

References

    1. Genetics. 1989 Nov;123(3):585-95 - PubMed

References

    1. Plant Sci. 2018 May;270:123-130 - PubMed

References

    1. Bioinformatics. 2007 Jul 15;23(14):1801-6 - PubMed

References

    1. PLoS One. 2017 Jun 7;12(6):e0179087 - PubMed

References

    1. Genetics. 2003 Aug;164(4):1567-87 - PubMed

References

    1. Front Plant Sci. 2017 Apr 18;8:575 - PubMed

References

    1. PLoS One. 2016 Feb 05;11(2):e0148671 - PubMed

References

    1. Breed Sci. 2013 Mar;63(1):49-57 - PubMed

LinkOut - more resources

Feedback