Ecological genomics of Chinese wheat improvement: implications in breeding for adaptation
Abstract Background China has diverse wheat varieties that adapt to very different environments divided into ten agro-ecological zones. A better understanding of genomic differences and patterns of selection among agro-ecological zones could provide useful information in selection of specific adapti...
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doaj-fcfbd4243abe496b8bef88f2755913112020-11-25T04:00:58ZengBMCBMC Plant Biology1471-22292020-10-0120111110.1186/s12870-020-02704-wEcological genomics of Chinese wheat improvement: implications in breeding for adaptationJie Guo0Chang Li1Junjie Zhao2Jiahui Guo3Weiping Shi4Shunhe Cheng5Meixue Zhou6Chenyang Hao7College of Agronomy, Shanxi Agricultural UniversityKey Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs/The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural SciencesKey Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs/The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural SciencesCollege of Agronomy, Shanxi Agricultural UniversityCollege of Agronomy, Shanxi Agricultural UniversityCollege of Agronomy, Shanxi Agricultural UniversityCollege of Agronomy, Shanxi Agricultural UniversityKey Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs/The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural SciencesAbstract Background China has diverse wheat varieties that adapt to very different environments divided into ten agro-ecological zones. A better understanding of genomic differences and patterns of selection among agro-ecological zones could provide useful information in selection of specific adaptive traits in breeding. Results We genotyped 438 wheat accessions from ten zones with kompetitive allele specific PCR (KASP) markers specific to 47 cloned genes for grain yield, quality, adaptation and stress resistance. Phylogenetic trees and principle component analysis revealed clear differences in winter and spring growth habits. Nucleotide diversity (π) and π ratio (π CL/π MCC) suggested that genetic diversity had increased during breeding, and that Chinese landraces (CL) from Zones I-V contributed little to modern Chinese cultivars (MCC). π ratio and Fst identified 24 KASP markers with 53 strong selection signals specific to Zones I (9 signals), II (12), III (5), IV (5), V (6), and VI (6). Genes with clear genetic differentiation and strong response to selection in at least three zones were leaf rust resistance gene Lr34 (I, II, III and IV), photoperiod sensitivity gene Ppd-D1 (I, II, III, IV and V), vernalization gene Vrn-B1 (V, VII, VIII and X), quality-related gene Glu-B1 (I, II and III) and yield-related genes Sus1-7B (I, II, III, IV and IX), Sus2-2A (I, II, III., IV and VI) and GW2-6B (II, V and VI). Conclusions This study examined selection of multiple genes in each zone, traced the distribution of important genetic variations and provided useful information for ecological genomics and enlightening future breeding goals for different agro-ecological zones.http://link.springer.com/article/10.1186/s12870-020-02704-wBread wheatAgro-ecological zonesSelectionKASP marker |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Jie Guo Chang Li Junjie Zhao Jiahui Guo Weiping Shi Shunhe Cheng Meixue Zhou Chenyang Hao |
spellingShingle |
Jie Guo Chang Li Junjie Zhao Jiahui Guo Weiping Shi Shunhe Cheng Meixue Zhou Chenyang Hao Ecological genomics of Chinese wheat improvement: implications in breeding for adaptation BMC Plant Biology Bread wheat Agro-ecological zones Selection KASP marker |
author_facet |
Jie Guo Chang Li Junjie Zhao Jiahui Guo Weiping Shi Shunhe Cheng Meixue Zhou Chenyang Hao |
author_sort |
Jie Guo |
title |
Ecological genomics of Chinese wheat improvement: implications in breeding for adaptation |
title_short |
Ecological genomics of Chinese wheat improvement: implications in breeding for adaptation |
title_full |
Ecological genomics of Chinese wheat improvement: implications in breeding for adaptation |
title_fullStr |
Ecological genomics of Chinese wheat improvement: implications in breeding for adaptation |
title_full_unstemmed |
Ecological genomics of Chinese wheat improvement: implications in breeding for adaptation |
title_sort |
ecological genomics of chinese wheat improvement: implications in breeding for adaptation |
publisher |
BMC |
series |
BMC Plant Biology |
issn |
1471-2229 |
publishDate |
2020-10-01 |
description |
Abstract Background China has diverse wheat varieties that adapt to very different environments divided into ten agro-ecological zones. A better understanding of genomic differences and patterns of selection among agro-ecological zones could provide useful information in selection of specific adaptive traits in breeding. Results We genotyped 438 wheat accessions from ten zones with kompetitive allele specific PCR (KASP) markers specific to 47 cloned genes for grain yield, quality, adaptation and stress resistance. Phylogenetic trees and principle component analysis revealed clear differences in winter and spring growth habits. Nucleotide diversity (π) and π ratio (π CL/π MCC) suggested that genetic diversity had increased during breeding, and that Chinese landraces (CL) from Zones I-V contributed little to modern Chinese cultivars (MCC). π ratio and Fst identified 24 KASP markers with 53 strong selection signals specific to Zones I (9 signals), II (12), III (5), IV (5), V (6), and VI (6). Genes with clear genetic differentiation and strong response to selection in at least three zones were leaf rust resistance gene Lr34 (I, II, III and IV), photoperiod sensitivity gene Ppd-D1 (I, II, III, IV and V), vernalization gene Vrn-B1 (V, VII, VIII and X), quality-related gene Glu-B1 (I, II and III) and yield-related genes Sus1-7B (I, II, III, IV and IX), Sus2-2A (I, II, III., IV and VI) and GW2-6B (II, V and VI). Conclusions This study examined selection of multiple genes in each zone, traced the distribution of important genetic variations and provided useful information for ecological genomics and enlightening future breeding goals for different agro-ecological zones. |
topic |
Bread wheat Agro-ecological zones Selection KASP marker |
url |
http://link.springer.com/article/10.1186/s12870-020-02704-w |
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