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Unlocking the novel genetic diversity and population structure of synthetic Hexaploid wheat.
BMC Genomics. 2018 Aug 06; 19(1):591.BG

Abstract

BACKGROUND

Synthetic hexaploid wheat (SHW) is a reconstitution of hexaploid wheat from its progenitors (Triticum turgidum ssp. durum L.; AABB x Aegilops tauschii Coss.; DD) and has novel sources of genetic diversity for broadening the genetic base of elite bread wheat (BW) germplasm (T. aestivum L). Understanding the diversity and population structure of SHWs will facilitate their use in wheat breeding programs. Our objectives were to understand the genetic diversity and population structure of SHWs and compare the genetic diversity of SHWs with elite BW cultivars and demonstrate the potential of SHWs to broaden the genetic base of modern wheat germplasm.

RESULTS

The genotyping-by-sequencing of SHW provided 35,939 high-quality single nucleotide polymorphisms (SNPs) that were distributed across the A (33%), B (36%), and D (31%) genomes. The percentage of SNPs on the D genome was nearly same as the other two genomes, unlike in BW cultivars where the D genome polymorphism is generally much lower than the A and B genomes. This indicates the presence of high variation in the D genome in the SHWs. The D genome gene diversity of SHWs was 88.2% higher than that found in a sample of elite BW cultivars. Population structure analysis revealed that SHWs could be separated into two subgroups, mainly differentiated by geographical location of durum parents and growth habit of the crop (spring and winter type). Further population structure analysis of durum and Ae. parents separately identified two subgroups, mainly based on type of parents used. Although Ae. tauschii parents were divided into two sub-species: Ae. tauschii ssp. tauschii and ssp. strangulate, they were not clearly distinguished in the diversity analysis outcome. Population differentiation between SHWs (Spring_SHW and Winter_SHW) samples using analysis of molecular variance indicated 17.43% of genetic variance between populations and the remainder within populations.

CONCLUSIONS

SHWs were diverse and had a clearly distinguished population structure identified through GBS-derived SNPs. The results of this study will provide valuable information for wheat genetic improvement through inclusion of novel genetic variation and is a prerequisite for association mapping and genomic selection to unravel economically important marker-trait associations and for cultivar development.

Authors+Show Affiliations

Department of Agronomy and Horticulture, University of Nebraska-Lincoln, 362D Plant Sciences Hall, Lincoln, NE, 68583, USA.International Maize and Wheat Improvement Center (CIMMYT), P.K. 39 Emek, 06511, Ankara, Turkey.Department of Agronomy and Horticulture, University of Nebraska-Lincoln, 362D Plant Sciences Hall, Lincoln, NE, 68583, USA.Wheat Genetics Resource Center, Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA.Department of Agronomy and Horticulture, University of Nebraska-Lincoln, 362D Plant Sciences Hall, Lincoln, NE, 68583, USA. pbaenziger1@unl.edu.

Pub Type(s)

Comparative Study
Journal Article

Language

eng

PubMed ID

30081829

Citation

Bhatta, Madhav, et al. "Unlocking the Novel Genetic Diversity and Population Structure of Synthetic Hexaploid Wheat." BMC Genomics, vol. 19, no. 1, 2018, p. 591.
Bhatta M, Morgounov A, Belamkar V, et al. Unlocking the novel genetic diversity and population structure of synthetic Hexaploid wheat. BMC Genomics. 2018;19(1):591.
Bhatta, M., Morgounov, A., Belamkar, V., Poland, J., & Baenziger, P. S. (2018). Unlocking the novel genetic diversity and population structure of synthetic Hexaploid wheat. BMC Genomics, 19(1), 591. https://doi.org/10.1186/s12864-018-4969-2
Bhatta M, et al. Unlocking the Novel Genetic Diversity and Population Structure of Synthetic Hexaploid Wheat. BMC Genomics. 2018 Aug 6;19(1):591. PubMed PMID: 30081829.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Unlocking the novel genetic diversity and population structure of synthetic Hexaploid wheat. AU - Bhatta,Madhav, AU - Morgounov,Alexey, AU - Belamkar,Vikas, AU - Poland,Jesse, AU - Baenziger,P Stephen, Y1 - 2018/08/06/ PY - 2018/05/15/received PY - 2018/07/30/accepted PY - 2018/8/8/entrez PY - 2018/8/8/pubmed PY - 2018/12/12/medline KW - Aegilops tauschii KW - Bread wheat KW - D-genome diversity KW - Genotype-by-sequencing KW - Single nucleotide polymorphism KW - Triticum turgidum SP - 591 EP - 591 JF - BMC genomics JO - BMC Genomics VL - 19 IS - 1 N2 - BACKGROUND: Synthetic hexaploid wheat (SHW) is a reconstitution of hexaploid wheat from its progenitors (Triticum turgidum ssp. durum L.; AABB x Aegilops tauschii Coss.; DD) and has novel sources of genetic diversity for broadening the genetic base of elite bread wheat (BW) germplasm (T. aestivum L). Understanding the diversity and population structure of SHWs will facilitate their use in wheat breeding programs. Our objectives were to understand the genetic diversity and population structure of SHWs and compare the genetic diversity of SHWs with elite BW cultivars and demonstrate the potential of SHWs to broaden the genetic base of modern wheat germplasm. RESULTS: The genotyping-by-sequencing of SHW provided 35,939 high-quality single nucleotide polymorphisms (SNPs) that were distributed across the A (33%), B (36%), and D (31%) genomes. The percentage of SNPs on the D genome was nearly same as the other two genomes, unlike in BW cultivars where the D genome polymorphism is generally much lower than the A and B genomes. This indicates the presence of high variation in the D genome in the SHWs. The D genome gene diversity of SHWs was 88.2% higher than that found in a sample of elite BW cultivars. Population structure analysis revealed that SHWs could be separated into two subgroups, mainly differentiated by geographical location of durum parents and growth habit of the crop (spring and winter type). Further population structure analysis of durum and Ae. parents separately identified two subgroups, mainly based on type of parents used. Although Ae. tauschii parents were divided into two sub-species: Ae. tauschii ssp. tauschii and ssp. strangulate, they were not clearly distinguished in the diversity analysis outcome. Population differentiation between SHWs (Spring_SHW and Winter_SHW) samples using analysis of molecular variance indicated 17.43% of genetic variance between populations and the remainder within populations. CONCLUSIONS: SHWs were diverse and had a clearly distinguished population structure identified through GBS-derived SNPs. The results of this study will provide valuable information for wheat genetic improvement through inclusion of novel genetic variation and is a prerequisite for association mapping and genomic selection to unravel economically important marker-trait associations and for cultivar development. SN - 1471-2164 UR - https://www.unboundmedicine.com/medline/citation/30081829/Unlocking_the_novel_genetic_diversity_and_population_structure_of_synthetic_Hexaploid_wheat_ L2 - https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-018-4969-2 DB - PRIME DP - Unbound Medicine ER -