Please wait a minute...
Journal of Integrative Agriculture  2022, Vol. 21 Issue (8): 2183-2196    DOI: 10.1016/S2095-3119(21)63699-7
Special Issue: 麦类遗传育种合辑Triticeae Crops Genetics · Breeding · Germplasm Resources
Crop Science Advanced Online Publication | Current Issue | Archive | Adv Search |
Allele mining of wheat ABA receptor at TaPYL4 suggests neo-functionalization among the wheat homoeologs
WU Bang-bang1*, SHI Meng-meng1*, Mohammad POURKHEIRANDISH2, ZHAO Qi1, WANG Ying1, YANG Chen-kang1, QIAO Ling1, ZHAO Jia-jia1, YAN Su-xian1, ZHENG Xing-wei1, ZHENG Jun1
1 Institute of Wheat Research, Shanxi Agricultural University, Linfen 041000, P.R.China
2 Plant Molecular Biology and Biotechnology Laboratory, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria 3010, Australia
Download:  PDF in ScienceDirect  
Export:  BibTeX | EndNote (RIS)      


Abstract  ABA receptors (PYR/PYL/RCAR) play a central role in the water loss control of plants.  A previous report indicated that TaPYL4 is a critical gene in wheat that improves grain production under drought conditions and increases water use efficiency.  In this study, we analyzed the sequence polymorphisms and genetic effects of TaPYL4s.  Based on isolated TaPYL4 genes from chromosomes 2A, 2B and 2D, three haplotypes were detected in the promoter region of TaPYL4-2A, and two haplotypes were present in TaPYL4-2B and TaPYL4-2D, respectively.  Marker/trait association analysis indicated that TaPYL4-2A was significantly associated with plant height in 262 Chinese wheat core collection accessions, as well as the drought tolerance coefficient (DTC) for plant height in 239 wheat varieties from Shanxi Province in multiple environments.  However, the frequencies of favored drought-tolerant haplotype TaPYL4-2A-Hap2 were considerably low, accounting for only 10%, and lines with this certain Hap could be reserved in the breeding program.  TaPYL4-2B was significantly associated with grain number, and the favored haplotype TaPYL4-2B-Hap1 was the dominant allele of above 90% in the collection.  For TaPYL4-2D, there were no significant differences in these traits between the two haplotypes in either of the two panels.  These results indicate that variation might lead to functional differentiation among the homoeologs and the haplotypes had undergone artificial selection during breeding.  Two molecular markers developed to distinguish these haplotypes could be used for breeding in water-limited regions.

Keywords:  TaPYL4        haplotypes       neo-functionalization        molecular markers  
Received: 26 November 2020   Accepted: 02 April 2021
Fund: This work was supported by the Agricultural Science Research of Shanxi Academy of Agricultural Sciences, China (YZGC013 and YCX2020BH2), and the Key Research and Development Program of Shanxi Province, China (201803D421021 and 201903D221074).
About author:  WU Bang-bang, E-mail:; Correspondence ZHENG Jun, Moblie: +86-18835712419, E-mail:; ZHENG Xing-wei, Mobile: +86-13467190463, E-mail: * These authors contributed equally to this study.

Cite this article: 

WU Bang-bang, SHI Meng-meng, Mohammad POURKHEIRANDISH, ZHAO Qi, WANG Ying, YANG Chen-kang, QIAO Ling, ZHAO Jia-jia, YAN Su-xian, ZHENG Xing-wei, ZHENG Jun. 2022. Allele mining of wheat ABA receptor at TaPYL4 suggests neo-functionalization among the wheat homoeologs. Journal of Integrative Agriculture, 21(8): 2183-2196.

Bennett D, Izanloo A, Reynolds M, Kuchel H, Langridge P, Schnurbusch T. 2012. Genetic dissection of grain yield and physical grain quality in bread wheat (Triticum aestivum L.) under water-limited environments. Theoretical and Applied Genetics, 125, 255–271.
Bernardo R. 1996a. Marker-based estimate of identity by descent and alikeness in state among maize inbreds. Theoretical and Applied Genetics, 93, 262–267.
Bernardo R. 1996b. Test cross additive and dominance effects in best linear unbiased prediction of maize single-cross performance. Theoretical and Applied Genetics, 93, 1098–1102.
Chang J Z, Zhang J N, Mao X G, Li A, Jia J Z, Jing R L. 2013. Polymorphism of TaSAP1-A1 and its association with agronomic traits in wheat. Planta, 237, 1495–1508.
Chen B R, Wang C Y, Wang P, Zhu Z X, Xu N, Shi G S, Yu M, Wang N, Li J H, Hou J M, Li S J, Zhou Y F, Gao S J, Lu X C, Huang R D. 2019. Genome-wide association study for starch content and constitution in sorghum (Sorghum bicolor (L.) Moench). Journal of Integrative Agriculture, 18, 2446–2456.
Chen F, Zhang F Y, Xia X C, Dong Z D, Cui D Q. 2012. Distribution of puroindoline alleles in bread wheat cultivars of the Yellow and Huai Valley of China and discovery of a novel puroindoline a allele without PINA protein. Molecular Breeding, 29, 371–378.
Cheng H, Liu J, Wen J, Nie X J, Xu L H, Chen N B, Li Z X, Wang Q L, Zheng Z Q, Li M, Cui L C, Liu Z H, Bian J X, Wang Z H, Xu S B, Yang Q, Apples R, Han D J, Song W N, Sun Q X, Jiang Y. 2019. Frequent intra- and inter-species introgression shapes the landscape of genetic variation in bread wheat. Genome Biology, 20, 1–16.
Dittrich M, Mueller H M, Bauer H, Peirats-Llobet M, Rodriguez P L, Geilfus C M, Carpentier S C, Rasheid K A S A, Kollist H, Merilo E, Herrmann J, Müller T, Ache P, Hetherington A M, Hedrich R. 2019. The role of Arabidopsis ABA receptors from the PYR/PYL/RCAR family in stomatal acclimation and closure signal integration. Nature Plants, 5, 1002–1011.
Dong Y, Zhang Y, Xiao Y G, Yan J, Liu J D, Wen W, Zhang Y, Jing R L, Xia X C, He Z H. 2016. Cloning of TaSST genes associated with water soluble carbohydrate content in bread wheat stems and development of a functional marker. Theoretical and Applied Genetics, 129, 1061–1070.
Gao Y J, An K X, Guo W W, Chen Y M, Zhang R J, Zhang X, Chang S Y, Rossi V, Jin F M, Cao X Y, Xin M M, Peng H R, Hu Z R, Guo W L, Du J K, Ni Z F, Sun Q X, Yao Y Y. 2021. The endosperm-specific transcription factor TaNAC019 regulates glutenin and starch accumulation and its elite allele improves wheat grain quality. The Plant Cell, 33, 603–622.
Gaston A P, Lesia R, Regina A, Miguel G G, Cristina Y, Ebe M, Hannes K, Armando A, Pedro L R. 2013. The PYL4 A194T mutant uncovers a key role of PYL4-PP2CA interaction for ABA signaling and plant drought resistance. Plant Physiology, 163, 441–455.
Geng S F, Li A L, Tang L C, Yin L J, Wu L, Lei C L, Guo X P, Zhang X, Jiang G H, Zhai W X, Wei Y M, Zheng Y L, Lan X J, Mao L. 2013. TaCPK2-A, a calcium-dependent protein kinase gene that is required for wheat powdery mildew resistance enhances bacterial blight resistance in transgenic rice. Journal of Experimental Botany, 64, 3125–3136.
Giroux M J, Morris C F. 1997. A glycine to serine change in puroindoline b is associated with wheat grain hardness and low levels of starch-surface friabilin. Theoretical and Applied Genetics, 95, 857–864.
Guo Z A, Song Y X, Zhou R H, Ren Z L, Jia J Z. 2010. Discovery, evaluation and distribution of haplotypes of the wheat Ppd-D1 gene. The New Phytologist, 185, 841–851. 
Hao C Y, Dong Y C, Wang L F, You G X, Zhang H N, Ge H M, Jia J Z, Zhang X Y. 2008. Genetic diversity and construction of core collection in Chinese wheat genetic resources. Chinese Science Bulletin, 53, 1518–1526.
Hao C Y, Jiao C Z, Hou J, Li T, Liu H X, Wang Y Q, Zheng J, Liu H, Bi Z H, Xu F F, Zhao J, Ma L, Wang Y M, Majeed U, Liu X, Appels R, Maccaferri M, Tuberosa R, Lu H F, Zhang X X. 2020. Resequencing of 145 cultivars reveals asymmetric sub-genome selection and strong founder genotype effects on wheat breeding in China. Molecular Plant, 13, 1733–1751. 
Hao C Y, Wang L F, Ge H M, Dong Y C, Zhang X Y. 2011. Genetic diversity and linkage disequilibrium in Chinese bread wheat (Triticum aestivum L.) revealed by SSR markers. PLoS ONE, 6, e17279.
He Y, Hao Q, Li W Q, Yan C Y, Yan N E, Yin P. 2014. Identification and characterization of ABA receptors in Oryza sativa. PLoS ONE, 9, e95246.
Huang J F, Li Long, Mao X G, Wang J Y, Liu H M, Li C N, Jing R L. 2020. dCAPS markers developed for nitrate transporter genes TaNRT2L12s associating with 1 000-grain weight in wheat. Journal of Integrative Agriculture, 19, 1543–1553.
Hyunmi K, Kyeyoon L, Hyunsik H, Nikita B, Dool Y K, In S Y, Myung O B, Sun T K, Jung K H, Beom G K. 2014. Overexpression of PYL5 in rice enhances drought tolerance, inhibits growth, and modulates gene expression. Journal of Experimental Botany, 65, 453–464.
IWGSC (International Wheat Genome Sequencing Consortium). 2018. Shifting the limits in wheat research and breeding using a fully annotated reference genome. Science, 361, eaar7191. 
Jordan K W, Wang S C, Lun Y N, Gardiner L J, MacLachlan R, Hucl P, Wiebe K, Wong D, Forrest K L, Sharpe A G, Sidebottom C H, Hall N, Toomajian C, Close T, Dubcovsky J, Akhunova A, Talbert L, Bansal U K, Bariana H S, Hayden M J, et al. 2015. A haplotype map of allohexaploid wheat reveals distinct patterns of selection on homoeologous genomes. Genome Biology, 16, 48.
Khan A R, Enjalbert J, Marsollier A C, Rousselet A, Goldringer I, Vitte C. 2013. Vernalization treatment induces site-specific DNA hypermethylation at the VERNALIZATION-A1 (VRN-A1) locus in hexaploid winter wheat. BMC Plant Biology, 13, 209.
Kumar A, Saripalli G, Jan I, Kumar K, Sharma P K, Balyan H S, Gupta P K. 2020. Meta-QTL analysis and identification of candidate genes for drought tolerance in bread wheat (Triticum aestivum L.). Physiology and Molecular Biology of Plants, 26, 1713–1725.
Lagudah E S, Krattinger S G, Herrera-Foessel S, Singh R P, Huerta-Espino J, Spielmeyer W, Brown-Guedira G, Selter L L, Keller B. 2009. Gene-specific markers for the wheat gene Lr34/Yr18/Pm38 which confers resistance to multiple fungal pathogens. Theoretical and Applied Genetics, 119, 889–898.
Li H H, Ribaut J M, Li Z L, Wang J K. 2008. Inclusive composite interval mapping (ICIM) for digenic epistasis of quantitative traits in biparental populations. Theoretical and Applied Genetics, 116, 243–260.
Liu Y C, Hou J, Wang X L, Li T, Majeed U, Hao C Y, Zhang X Y. 2020. The NAC transcription factor NAC019-A1 is a negative regulator of starch synthesis in wheat developing endosperm. Journal of Experimental Botany, 71, 5794–5807.
Liu Y N, He Z H, Appels R, Xia X C. 2012. Functional markers in wheat: Current status and future prospects. Theoretical and Applied Genetics, 125, 1–10.
Ma D Y, Yan J, He Z H, Wu L, Xia X C. 2012. Characterization of a cell wall invertase gene Tacwi-A1 on common wheat chromosome 2A and development of functional markers. Molecular Breeding, 29, 43–52.
Ma L, Hao C Y, Liu H X, Hou J, Lia T, Zhang X Y. 2019. Diversity and sub-functionalization of TaGW8 homoeologs hold potential for genetic yield improvement in wheat. The Crop Journal, 7, 830–844.
Mega R, Abe F, Kim JS, Tsuboi Y, Tanaka K, Kobayashi H, Sakata Y, Hanada K, Tsujimoto H, Kikuchi J, Cutler S R, Okamoto M. 2019. Tuning water-use efficiency and drought tolerance in wheat using abscisic acid receptors. Nature Plants, 5, 153–159.
Montenegro J D, Golicz A A, Bayer P E, Hurgobin B, Lee H T, Chan C K, Visendi P, Lai K, Doležel J, Batley J, Edwards D. 2017. The pangenome of hexaploid bread wheat. Plant Journal, 90, 1007–1013.
Murai J, Taira T, Ohta D. 1999. Isolation and characterization of the three Waxy genes encoding the granule-bound starch synthase in hexaploid wheat. Gene, 234, 71–79.
Park S Y, Fung P, Nishimura N, Jensen D R, Fujii H, Zhao Y, Lumba S, Santiago J, Rodrigues A, Chow T F, Alfred S E, Bonetta D, Finkelstein R, Provart N J, Desveaux D, Rodriguez P L, McCourt P, Zhu J K, Schroeder J I, Volkman B F, et al. 2009. Abscisic acid inhibits type 2C protein phosphatases via the PYR/PYL family of START proteins. Science, 324, 1068–1071.
Pourkheirandish M, Golicz A A, Bhalla P L, Singh M B. 2020. Global role of crop genomics in the face of climate change. Frontiers in Plant Science, 11, 922.
Qin L, Zhao J J, Li T, Hou J, Zhang X Y, Hao C Y. 2017. TaGW2, a good reflection of wheat polyploidization and evolution. Frontiers in Plant Science, 8, 318.
Su Z Q, Hao C Y, Wang L F, Dong Y C, Zhang X Y. 2011. Identification and development of a functional marker of TaGW2 associated with grain weight in bread wheat (Triticum aestivum L.). Theoretical and Applied Genetics, 122, 211–223.
Tommasini L, Yahiaoui N, Srichumpa P, Keller B. 2006. Development of functional markers specific for seven Pm3 resistance alleles and their validation in the bread wheat gene pool. Theoretical and Applied Genetics, 114, 165–175.
Tura H, Edwards J, Gahlaut V, Garcia M, Sznajder B, Baumann U, Shahinnia F, Reynolds M, Langridge P, Balyan H S, Gupta P K, Schnurbusch T, Fleury D. 2020. QTL analysis and fine mapping of a QTL for yield-related traits in wheat grown in dry and hot environments. Theoretical and Applied Genetics, 133, 239–257.
Wang H W, Yin H Y, Jiao C Z, Fang X J, Wang G P, Li G R, Ni F, Li P H, Su P S, Ge W Y, Lyu Z F, Xu S S, Yang Y H, Hao Y C, Cheng X X, Zhao J X, Liu C, Xu F F, Ma X, Sun S L, et al. 2020. Sympatric speciation of wild emmer wheat driven by ecology and chromosomal rearrangements. Proceedings of the National Academy of Sciences of the United States of America, 117, 5955–5963.
Wang H Y, Wang S G, Chang X P, Hao C Y, Sun D Z, Jing R L. 2019. Identification of TaPPH–7A haplotypes and development of a molecular marker associated with important agronomic traits in common wheat. BMC Plant Biology, 19, 1–12.
Wei B, Jing R L, Wang C S, Chen J B, Mao X G, Chang X P, Jia J Z. 2009. Dreb1 genes in wheat (Triticum aestivum L.): Development of functional markers and gene mapping based on SNPs. Molecular Breeding, 23, 13–22.
Wendel J F. 2000. Genome evolution in polyploids. Plant Molecular Biology, 42, 225–249.
Yue A Q, Li A, Mao X G, Chang X P, Li R Z, Jing R L. 2015. Identification and development of a functional marker from 6-SFT-A2 associated with grain weight in wheat. Molecular Breeding, 35, 63–73.
Zhai H J, Jiang C C, Zhao Y, Yang S L, Li Y W, Yan K F, Wu S Y, Luo B K, Du Y, Jin H B, Liu X, Zhang Y B, Lu F, Reynolds M, Ou X Q, Qiao W C, Jiang Z K, Peng T, Gao D R, Hu W J, et al. 2021. Wheat heat tolerance is impaired by heightened deletions in the distal end of 4AL chromosomal arm. Plant Biotechnology Journal, 1–14.
Zhang B, Xu W N, Liu X, Mao X G, Li A, Wang J Y, Chang X P, Zhang X Y, Jing R L. 2017. Functional conservation and divergence among homoeologs of TaSPL20 and TaSPL21, two SBP-box genes governing yield-related traits in hexaploid wheat. Plant Physiology, 174, 1177–1191.
Zhang Y, Li D, Zhang D B, Zhao X G, Cao X M, Dong L L, Liu J X, Chen K L, Zhang H W, Gao C X, Wang D W. 2018. Analysis of the functions of TaGW2 homoeologs in wheat grain weight and protein content traits. The Plant Journal for Cell and Molecular Biology, 94, 857–866.
Zhao J J, Qiao L, Wu B B, Ge C, Qiao L Y, Zhang S W, Yan S X, Zheng X W, Zheng J. 2020a. Seedling root characteristics and drought resistance of wheat in Shanxi Province. Acta Agronomica Sinica, 47, 714–727. (in Chinese)
Zhao J J, Zheng X W, Qiao L, Ge C, Wu B B, Zhang S W, Qiao L Y, Feng Z W, Zheng J. 2020b. Effects of HMW-GSs on quality related traits in wheat (Triticum aestivum L.) under different water regimes. PLoS ONE, 15, e0237711.
Zheng J, Liu H, Wang Y Q, Wang L F, Chang X P, Jing R L, Hao C Y, Zhang X Y. 2014. TaTEF–7A, a transcript elongation factor influences yield-related traits in bread wheat (Triticum aestivum L.). Journal of Experimental Botany, 65, 5351–5365.
Zheng X W, Liu C, Qiao L, Zhao J J, Han R, Wang X L, Ge C, Zhang W Y, Zhang S W, Qiao L Y, Zheng J, Hao C Y. 2020. The MYB transcription factor TaPHR3-A1 is involved in phosphate signaling and governs yield-related traits in bread wheat (Triticum aestivum L.). Journal of Experimental Botany, 71, 5808–5822.
Zheng X W, Wen X J, Qiao L, Zhao J J, Zhang X J, Li X, Zhang S W, Yang Z J, Chang Z J, Chen J L, Zheng J. 2019. A novel QTL QTrl.saw–2D.2 associated with the total root length identified by linkage and association analyses in wheat (Triticum aestivum L.). Planta, 250, 129–143.
Zhou Y, Zhao X B , Li Y W, Xu J, Bi  A Y, Kang L P, Xu D X , Chen H F, Wang Y, Wang Y G, Liu S Y, Jiao C Z, Lu H F, Wang J, Yin C B, Jiao Y L, Lu  F. 2020. Triticum population sequencing provides insights into wheat adaptation. Nature Genetics, 52, 1412–1422.

No related articles found!
No Suggested Reading articles found!