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Genetic Diversity, Population Structure and Marker-Trait Associations For Wang et al. BMC Plant Biology (2017) 17:112 DOI 10.1186/s12870-017-1058-7 RESEARCH ARTICLE Open Access Genetic diversity, population structure and marker-trait associations for agronomic and grain traits in wild diploid wheat Triticum urartu Xin Wang1,2, Guangbin Luo1,2, Wenlong Yang1, Yiwen Li1, Jiazhu Sun1, Kehui Zhan3, Dongcheng Liu1* and Aimin Zhang1,3* Abstract Background: Wild diploid wheat, Triticum urartu (T. urartu) is the progenitor of bread wheat, and understanding its genetic diversity and genome function will provide considerable reference for dissecting genomic information of common wheat. Results: In this study, we investigated the morphological and genetic diversity and population structure of 238 T. urartu accessions collected from different geographic regions. This collection had 19.37 alleles per SSR locus and its polymorphic information content (PIC) value was 0.76, and the PIC and Nei’s gene diversity (GD) of high-molecular- weight glutenin subunits (HMW-GSs) were 0.86 and 0.88, respectively. UPGMA clustering analysis indicated that the 238 T. urartu accessions could be classified into two subpopulations, of which Cluster I contained accessions from Eastern Mediterranean coast and those from Mesopotamia and Transcaucasia belonged to Cluster II. The wide range of genetic diversity along with the manageable number of accessions makes it one of the best collections for mining valuable genes based on marker-trait association. Significant associations were observed between simple sequence repeats (SSR) or HMW-GSs and six morphological traits: heading date (HD), plant height (PH), spike length (SPL), spikelet number per spike (SPLN), tiller angle (TA) and grain length (GL). Conclusions: Our data demonstrated that SSRs and HMW-GSs were useful markers for identification of beneficial genes controlling important traits in T. urartu, and subsequently for their conservation and future utilization, which may be useful for genetic improvement of the cultivated hexaploid wheat. Keywords: Triticum urartu, Genetic diversity, SSR markers, HMW-GS, Marker-trait association Background components is a pre-requisite, though genomic research Bread wheat (Triticum aestivum L.) is one of the most in bread wheat remains a major challenge because of the important crops in the world, providing about 20% of complexity associated with its hexaploid structure and the calories consumed globally (FAOSTAT 2011; http:// huge genome size [2, 3]. Wild diploid wheat, T. urartu faostat.fao.org/). To meet the world’s growing demand (2n =2× =14; AA), the A-genome donor of cultivated for food, it is urgent to develop high yielding varieties tetraploid (2n =4× =28; genome AABB) and hexaploid with good end-product making quality [1]. A better wheat (2n =6× =42; AABBDD) [4], played an important understanding of the genetic basis of yield and its role in the development and evolution of cultivated bread wheat. With the available reference genome [5], it * Correspondence: [email protected]; [email protected] is more feasible to exploit T. urartu as the reference 1 State Key Laboratory of Plant Cell and Chromosome Engineering, National sub-genome of common wheat, which will obviously Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 1 West Beichen Road, Chaoyang provide considerable valuable information for the im- District, Beijing 100101, China provement of the latter. Full list of author information is available at the end of the article © The Author(s). 2017 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Wang et al. BMC Plant Biology (2017) 17:112 Page 2 of 17 Although T. urartu possesses the A genome in com- Methods mon with bread wheat, its genetic diversity has not been Plant material well investigated as Einkorn wheat (T. monococcum), A total of 238 T. urartu accessions, which covered most another diploid progenitor [6]. Nowadays, the genetic of the original areas, were subjected to SSR and high- diversity within wheat cultivars has been drastically molecular-weight glutenin subunits (HMW-GS) analysis reduced in the process of domestication and breeding with SDS-PAGE. This panel was obtained from the Insti- [7, 8], and it is essential to apply new contributing tute of Genetics and Developmental Biology, Chinese genes for wheat improvement. As a wild diploid pro- Academy of Sciences (IGDB, CAS), the National Small genitor of hexaploid wheat, T. urartu harbors rich al- Grain collection (USDA-ARS) and the International lelic diversity for numerous important traits, including Center for Agricultural Research in the Dry Areas agronomic characteristics, grain quality and biotic (ICARDA). Among these accessions, 84 were originated stress tolerance [9–11]. Genetic variation of T. urartu from Lebanon, 80 from Turkey, 37 from Syria, 12 from has been investigated using various markers such as Armenia, 11 from Jordan, 11 from Iran, and three from isozyme, restriction fragment length polymorphism Iraq (Fig. 1; Additional file 1: Table S1). (RFLP), amplified fragment length polymorphism (AFLP), and random amplified polymorphic DNA Field experiment and phenotyping (RAPD) markers [12–16]. Such genetic diversities can The collected T. urartu accessions were planted at the be exploited to elucidate the genetic basis of natural experimental station of the Institute of Genetics and Devel- variation of important quantitative traits. Hence, more opmental Biology, Chinese Academy of Sciences, Beijing accessions widespread should be employed to provide (40°5′56″N and 116°25′8″E), that of Henan Agricultural a more comprehensive on the characteristic of the University, Zhengzhou (34°51′52″N, 113°35′45″E) and whole population. that of Dezhou Academy of Agricultural Sciences, Dezhou Most agronomic traits in common wheat, such as yield (37°45′69″N, 116°30′23″E) in two consecutive years and its components, dough quality and resistant charac- (2013-2014 and 2014-2015 cropping seasons). These ters, are controlled by multiple genes and influenced sub- environments were designated as E1 (Beijing, 2013), E2 stantially by the environment, which hinders the (Zhengzhou, 2013), E3 (Dezhou, 2013), E4 (Beijing, 2014), dissection of their genetic basis [17]. Classical linkage E5 (Zhengzhou, 2014), and E6 (Dezhou, 2014), respectively. mapping based on bi-parental populations was a conven- Each field trial was managed in a completely random- tional approach to dissect the genetic bases of complex ized block design with two replications. All the plants traits [18]. Various studies have identified a set of major were grown in a single 2-m row with 40 cm between effect quantitative trait loci (QTL) for important agro- rows and 20 cm between individuals. Nine traits were nomic traits in wheat, such as kernel weight and dough evaluated and analyzed, including heading date (HD), quality [17, 19–24]. As an alternative way to QTL map- plant height (PH), spike length (SPL), spikelet number ping, association mapping uses diverse material to associ- per spike (SPLN), tiller angle (TA), grain length (GL), ate genetic markers with a phenotype of interest, which grain width (GW), grain length/width ratio (GLW) and presents higher mapping resolution of the phenotypes at a thousand-grain weight (TGW). The HD was counted as population level [25]. It has been exploited successfully to days from sowing to heading, and the date of heading identify genomic regions contributing to numerous traits was subsequently recorded when half of the spikes in diverse crops, such as maize [26, 27], rice [28], sorghum emerged from the flag leaf in each accession. The TA [29] and soybean [30]. There is increasing interests in was measured between the last developed tillers and the identifying novel marker-trait associations using associ- ground level with a protractor at the maximum tillering ation mapping in wheat [31, 32]. For example, Breseghello stage, while the other agronomic traits were determined and Sorrells [17] found significant associations between on the primary tiller. After the harvest, a minimum of some simple sequence repeats (SSR) markers and wheat 200 grains from each sample was photographed on a kernel traits, including weight, length and width of kernels. flat-bed scanner and the images were obtained as the The objectives of this study were to investigate the aerial view of the ventral side of the grains. The GL, GW genetic diversity, population structure and relationships and GLW were calculated using the grain analyzer soft- among a collection of 238 T. urartu accessions collected ware (SC-G Scanner, Wanshen Detection Technology from the Fertile Crescent region and to identify Inc., Hangzhou, China), and the TGW was measured by marker loci associated with important agronomic and the average of two 1000 kernel-weights. grain traits. Our results would provide further in- sights into the utility of association mapping for DNA isolation and nested-PCR amplification marker-assisted selection and its potential application Genomic DNA was isolated from young leaf tissue of in bread wheat breeding. two-week-old seedlings (one individual per accession) Wang et al. BMC Plant Biology (2017) 17:112 Page 3 of 17 Fig. 1 Geographic distribution of the T. urartu accessions used in this study. Green colors represent the locations of eastern Mediterranean coastal populations; Red colors represent the locations of Mesopotamia-Transcaucasia populations. The original map was freely downloaded from the website (http://sc.jb51.net/Web/Vector/qita/127830.html) using the cetyl trimethyl ammonium bromide (CTAB) before adding HiDi-formamide. Fluorescently labeled method [33].
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