Abstract
Wheat kernel morphology is a very important trait for wheat yield improvement. This is the first report of association analysis of kernel morphology traits in wheat breeding lines. In Qinghai, China, the research described here involved genome-wide association analysis in breeding lines derived from synthetic hexaploid wheat with a mixed linear model to identify the quantitative trait loci (QTLs) related to kernel morphology. The 8033 effective Diversity Array Technology (DArT) markers produced a genetic map of 5901.84 cM with an average density of 1.36 markers/cM. Population structure analysis classified 507 breeding lines into three groups by Bayesian structure analysis using unlinked markers. Linkage disequilibrium decay was observed with a map coverage of 2.78 cM. Marker-trait association analysis showed that 15 DArT markers for kernel morphology were detected, located on nine chromosomes, and explained 2.6%–4.0% of the phenotypic variation of kernel area (KA), kernel width (KW), kernel length (KL) and thousand-kernel weight (TKW). The marker 1139297 was related to both the KL and KA traits. Only six DArT markers were close to known QTLs. The parent SHW-L1 carried eight favored alleles, while other seven favored alleles were derived from elite common wheat cultivars. These QTLs, identified in elite breeding lines, should help us understand the kernel morphology trait better, and to provide germ-plasm for breeding new wheat cultivars for Qinghai Province or other regions.
Article PDF
Similar content being viewed by others
Avoid common mistakes on your manuscript.
References
Akbari, M., Wenzl, P., Caig, V., Carling, J., Xia, L., Yang, S., Uszynski, G., Mohler, V., Lehmensiek, A., Kuchel, H. 2006. Diversity arrays technology (DArT) for high-throughput profiling of the hexaploid wheat genome. Theor. Appl. Genet. 113:1409–1420.
Bordes, J., Goudemand, E., Duchalais, L., Chevarin, L., Oury, X.F., Heumez, E., Lapierre, A., Perretant, M.R., Rolland, B., Beghin, D., Laurent, V., Gouis, J.L., Storlie, E., Robert, O., Charmet, G. 2014. Genome-wide association mapping of three important traits using bread wheat elite breeding populations. Mol. Breed. 4:755–768.
Börner, A.E., Schumann, A., Fürste, H., Cöster, B., Leithold, M.S., Röder, W.E. 2002. Mapping of quantitative trait loci determining agronomic important characters in hexaploid wheat (Triticum aestivum L.). Theor. Appl. Genet. 105:921–936.
Bradbury, P.J., Zhang, Z., Kroon, D.E., Casstevens, T.M., Ramdoss, Y., Buckler, E.S. 2007. TASSEL: software for association mapping of complex traits in diverse samples. Bioinformatics. 23:2633–2635.
Calderini, D.F., Reynolds, M.P., Calderini, D.F., Reynolds, M.P. 2000. Changes in grain weight as a consequence of de-graining treatmentsat pre- and post-anthesis in synthetic hexaploid wheats. Aust. J. Plant Physiol. 27:183–191.
Chen, D.Z. 1993. New progress of wheat cultivation in China. Agriculture Press, Beijing, pp. 327–340 (in Chinese).
Cui, F., Fan, X.L., Chen, M., Zhang, N., Zhao, C.H., Zhang, W., Han, J., Ji, J., Zhao, X., Yang, L., Wang, T., Li, J.M. 2015. QTL detection for wheat kernel size and quality and the responses of these traits to low nitrogen stress. Theor. Appl. Genet. 129:469
Cui, F., Zhao, C.H., Ding, A.M., Li, J., Wang, L., Li, X.F., Bao, Y.G., Li, J.M., Wang, H.G. 2014. Construction of an integrative linkage map and QTL mapping of grain yield-related traits using three related wheat RIL populations. Theor. Appl. Genet. 127:659–675.
Das, M.K., Bai, G., Mujeeb-Kazi, A., Rajaram, S. 2016. Genetic diversity among synthetic hexaploid wheat accessions (Triticum aestivum) with resistance to several fungal diseases. Genet. Resour. Crop. Ev. 63:1285–1296.
Dreccer, M.F., Borgognone, M.G., Ogbonnaya, F.C., Trethowan, R.M., Winter, B. 2007. CIMMYT-selected derived synthetic bread wheats for rainfed environments: Yield evaluation in Mexico and Australia. Field Crops Res. 100:218–228.
Emebiri, L.C., Ogbonnaya, F.C. 2015. Exploring the synthetic hexaploid wheat for novel sources of tolerance to excess boron. Mol. Breed. 35:1–10.
Emebiri, L.C., Oliver, J.R., Mrva, K., Mares, D. 2010. Association mapping of late maturity α-amylase (LMA) activity in a collection of synthetic hexaploid wheat. Mol. Breed. 26:39–49.
Evers, A.D., Cox, R.I., Shaheedullah, M.Z., Withey, R.P. 1990. Predicting milling extraction rate by image analysis of wheat grains. Aspects Appl. Biol. 25:417–426.
Flint-Garcia, S.A., Thornsberry, J.M., Buckler, E.S. 2003. Structure of linkage disequilibrium in plants. Annu. Rev. Plant Physiol. 54:357–374.
Ginkel, M.V., Ogbonnaya, F. 2007. Novel genetic diversity from synthetic wheats in breeding cultivars for changing production conditions. Field Crops Res. 104:86–94.
Hawkesford, M.J., Araus, J.L., Park, R., Calderini, D., Miralles, D., Shen, T., Zhang, J., Parry, M.A.J. 2013. Prospects of doubling global wheat yields. Food and Energy Security. 2:34–48.
Li, J., Wan, H., Yang, W. 2014. Synthetic hexaploid wheat enhances variation and adaptive evolution of bread wheat in breeding processes. J. Syst. Evol. 52:735–742.
Neumann, K., Kobiljski, B., Denčić, S., Varshney, R., Börner, A. 2011. Genome-wide association mapping: a case study in bread wheat (Triticum aestivum L.). Mol Breed. 27:37–58.
Ogbonnaya, F.C., Abdalla, O., Mujeeb-Kazi, A., Kazi, A.G., Xu, S.S., Gosman, N., Lagudah, E.S., Bonnett, D., Sorrells, M.E., Tsujimoto, H. 2013. Synthetic hexaploids: harnessing species of the primary gene pool for wheat improvement. John Wiley & Sons, Inc. pp. 35–122.
Pritchard, J.K., Stephens, M., Rosenberg, N.A., Donnelly, P. 2000. Association mapping in structured populations. The American Journal of Human Genetics. 67:170–181.
Rasheed, A., Xia, X.C., Ogbonnaya, F., Mahmood, T., Zhang, Z.W., Mujeeb-Kazi, A. He, Z.H. 2014. Genome-wide association for grain morphology in synthetic hexaploid wheats using digital imaging analysis. BMC Plant Biology. 14:128
Sukumaran, S., Xiang, W., Bean, S.R., Pedersen, J.F., Kresovich, S., Tuinstra, M.R., Tesso, T.T., Hamblin, M.T., Yu, J.M. 2012. Association mapping for grain quality in a diverse sorghum collection. Plant Genome. 5:126–135.
Tang, Y., Wu, X.L., Li, C.S., Yang, W.Y., Huang, M.B., Ma, X.L., Li, S.Z. 2017. Yield, growth, canopy traits and photosynthesis in high-yielding, synthetic hexaploid-derived wheats cultivars compared with non-synthetic wheats. Crop & Pasture Science 68:115–125.
Wang, L.F., Ge, H.M., Hao, C.Y., Dong, Y.S., Zhang, X.Y. 2012. Identifying Loci Influencing 1,000-Kernel Weight in Wheat by Microsatellite Screening for Evidence of Selection during Breeding. PLoS One. 7:e29432.
Williams, K., Munkvold, J., Sorrells, M. 2013. Comparison of digital image analysis using elliptic Fourier descriptors and major dimensions to phenotype seed shape in hexaploid wheat (Triticum aestivum L.). Euphytica. 190:99–116.
Xiao, Y.G., Qiang, Z.G., Wu, K., Liu, J.J., Xia, X.C., Ji, W.Q., He, Z.H. 2012. Genetic gains in grain yield and physiological traits of winter wheat in Shandong province, China, from 1969 to 2006. Crop Sci. 52:44–56.
Yang, W., Liu, D., Li, J., Zhang, L., Wei, H., Hu, X., Zheng, Y., He, Z., Zou, Y. 2009. Synthetic hexaploid wheat and its utilization for wheat genetic improvement in China. J. Genet. Genomics. 36:539–546.
Yan, L., Liang, F., Xu, H., Zhang, X., Zhai, H., Sun, Q., Ni, Z. 2017. Identification of QTL for grain size and shape on the D genome of natural and synthetic allohexaploid wheat with near-identical AABB genomes. Front. Plant Sci. 8:1705
Yan, Z., Wan, Y., Liu, K., Zheng, Y., Wang, D. 2002. Identification of a novel HMW glutenin subunit and comparison of its amino acid sequence with those of homologous subunits. Chinese Sci. Bull. 47:220–225.
Yu, J., Pressoir, G., Briggs, W.H., Vroh, B.I., Yamasaki, M., Doebley, J.F., Mcmullen, M.D., Gaut, B.S., Nielsen, D.M., Holland, J.B., Kresovich, S., Buckler, E.S. 2006. A unified mixed-model 24 method for association mapping that accounts for multiple levels of relatedness. Nat. Genet. 38:203–208.
Zhang, H.X., Zhang, F.N., Li, G.D., Zhang, S.N., Zhang, Z.G., Ma, L.J. 2017. Genetic diversity and association mapping of agronomic yield traits in eighty six synthetic hexaploid wheat. Euphytica, 213:111
Zhang, L., Liu, D., Yan, Z., Lan, X., Zheng, Y., Zhou, Y. 2004. Rapid changes of microsatellite flanking sequence in the allopoh ploidization of new synthesized hexaploid wheat. Science in China. 47:553–561.
Zhang, K.P., Wang, J.J., Zhang, L.Y., Rong, C.W., Zhao, F.W., Peng, T., Li, H.M., Cheng, D.M., Liu, X., Qin, H.J. 2013. Association Analysis of Genomic Loci Important for Grain Weight Control in Elite Common Wheat Varieties Cultivated with Variable Water and Fertiliser Supply. PLoS One. 8:e57853–e57853
Author information
Authors and Affiliations
Corresponding authors
Additional information
Communicated by A. Börner
Electronic supplementary material
Rights and permissions
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.
About this article
Cite this article
Wang, H., Cao, D., Chen, W. et al. Genome-wide Association Analysis of Kernel Morphology in Breeding Lines Derived from Synthetic Hexaploid Wheat in Qinghai Province, China. CEREAL RESEARCH COMMUNICATIONS 46, 399–411 (2018). https://doi.org/10.1556/0806.46.2018.022
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1556/0806.46.2018.022