Identification of genetic loci and a candidate gene related to flag leaf traits in common wheat by genome-wide associati
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Identification of genetic loci and a candidate gene related to flag leaf traits in common wheat by genome-wide association study and linkage mapping Xuefang Yan & Lei Zhao & Yan Ren & Ning Zhang & Zhongdong Dong & Feng Chen
Received: 23 March 2020 / Accepted: 6 May 2020 # Springer Nature B.V. 2020
Abstract Flag leaf traits influence wheat yield by affecting photosynthetic capacity and plant architecture. In this study, flag leaf traits over 4 years in Chinese common wheat were investigated for genome-wide association study (GWAS) analysis using the wheat 90 K SNP array. A total of 618 significant SNPs were identified in 9 environments and 36 of them are significant in at least three environments and BLUP (best linear unbiased prediction). Linkage mapping indicated that 23 QTL regulating flag leaf traits were detected in a biparental population with 5.8 to 28.7% phenotypic variation explained, respectively. Further analysis of multienvironmentally significant SNP revealed a candidate gene TaFLL-5B1 (TraesCS5B02G390300) related to flag leaf length (FLL). Sequencing results indicated that a 40-bp InDel (insertion/deletion) was identified in TaFLL-5B1 gene of different wheat cultivars. Association analysis showed that cultivars with TaFLL-5B1a (with a 40-bp InDel) showed significantly longer FLL than those with TaFLL-5B1b (without a 40-bp InDel).
Xuefang Yan and Lei Zhao contributed equally to this work. Electronic supplementary material The online version of this article (https://doi.org/10.1007/s11032-020-01135-7) contains supplementary material, which is available to authorized users. X. Yan : L. Zhao : Y. Ren : N. Zhang : Z. Dong : F. Chen (*) Agronomy College/National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, 15 Longzihu College District, Zhengzhou 450046, People’s Republic of China e-mail: [email protected]
EMS-mutagenized tetraploid wheat line Kronos2282 with premature stop codon of TaFLL-5B1 gene showed significantly shorter FLL than wild type. It suggests that TaFLL-5B1 possibly plays a key role in modulating wheat flag leaf traits. This research increases our understanding of the genetic basis of flag leaf traits and provides genetic loci potentially useful in breeding programs focused on improving wheat architecture and yield. Keywords Common wheat . GWAS . Linkage mapping . Flag leaf traits
Introduction Wheat is an important food crop and its agronomic traits have been thoroughly studied (Tian et al. 2011). The flag leaf of wheat usually refers to the last leaf to emerge before heading or the first leaf below the ear. It is the main functional leaf for photosynthesis in grain production. The flag leaf contributes almost 50% of the total plant photosynthesis (Liu et al. 2018a) and makes an important contribution to yield. The carbohydrates in wheat grains are mainly derived from the flag leaf (Hussain et al. 2017; Liu et al. 2018a). Flag leaf traits are significantly correlated with yield component traits such as thousand grain weight (TKW) and total spike number (Jia
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