Ecological genomics of Chinese wheat improvement: implications in breeding for adaptation
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RESEARCH ARTICLE
Open Access
Ecological genomics of Chinese wheat improvement: implications in breeding for adaptation Jie Guo1, Chang Li2, Junjie Zhao2, Jiahui Guo1, Weiping Shi1, Shunhe Cheng1,3, Meixue Zhou1,4 and Chenyang Hao2*
Abstract Background: China has diverse wheat varieties that adapt to very different environments divided into ten agroecological 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 (πCL/πMCC) 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. Keywords: Bread wheat, Agro-ecological zones, Selection, KASP marker
Background China is the largest wheat producer and consumer in the world. The wheat-growing areas are somewhat arbitrarily divided into ten agro-ecological zones each having varieties with different reactions to temperature, photoperiod, and biotic and abiotic stresses [1]. Autumn-sown * Correspondence: [email protected] 2 Key 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 Sciences, Beijing 100081, China Full list of author information is available at the end of the article
varieties account for approximately 90% of the production and area across Zones I (4% of the total production area), II (60%), III (13%), IV (10%) and V (minor area of production), whereas spring-sown wheats cover only 7% of the total area across Zones VI, VII and VIII. Zones IX and X have both autumn-sown and spring-sown wheats, but spring-sown wheat in these areas represents only 3% of the total wh
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