普通小麦科农9204高产潜力关键区段的解析

doi:10.1016/j.jia.2023.02.013

Journal of Integrative Agriculture ›› 2023, Vol. 22 ›› Issue (9): 2603-2616.DOI: 10.1016/j.jia.2023.02.013

普通小麦科农9204高产潜力关键区段的解析

收稿日期:2022-09-02 接受日期:2022-11-14 出版日期:2023-09-20 发布日期:2023-09-20

Dissecting the key genomic regions underlying high yield potential in common wheat variety ‘Kenong 9204’

ZHAO Chun-hua^1*, ZHANG Na^2*, FAN Xiao-li³, JI Jun^{4, 5}, SHI Xiao-li⁴, CUI Fa^1#, LING Hong-qing^4#, LI Jun-ming^{5, 6#}

¹ College of Agriculture, Ludong University/Key Laboratory of Molecular Module-based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, Yantai 264025, P.R.China
² Jiangsu Xuhuai Regional Institute of Agricultural Sciences, Xuzhou 221131, P.R.China
³Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, P.R.China
⁴ State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijng 100101, P.R.China
⁵ Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050022, P.R.China
⁶ Key Laboratory of Molecular and Cellular Biology, Ministry of Education/Hebei Collaboration Innovation Center for Cell Signaling/Hebei Key Laboratory of Molecular and Cellular Biology/College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, P.R.China

Received:2022-09-02 Accepted:2022-11-14 Online:2023-09-20 Published:2023-09-20
About author:ZHAO Chun-hua, E-mail: sdauzch@126.com; ZHANG Na, zhangna2nina@163.com; #Correspondence CUI Fa, Tel: +86-535-6223193, E-mail: sdaucf@126.com; LING Hong-qing, E-mail: hqling@genetics.ac.cn; LI Jun-ming, E-mail: ljm@sjziam.ac.cn * These authors contributed equally to this study.
Supported by:
This research was jointly supported by the grants from the Shandong Major Basic Research Project of Natural Science Foundation, China (ZR2019ZD16), the Shandong Provincial Key Research and Development Program, China (2019GNC106126 and 2021LZGC009), the Natural Science Foundation of Hebei Province, China (C2021205013), the Hebei Scientific and Technological Innovation Team of Modern Wheat Seed Industry, China (21326318D), the National Natural Science Foundation of China (31871612, 31901535, and 32101726), and the China Agriculture Research System of MOF and MARA (CARS-03).

摘要/Abstract

摘要：

骨干亲本在改良小麦产量和品质利用方面发挥重要作用。研究骨干亲本中某些有益性状的遗传基础将为分子育种提供理论参考。科农9204是具有理想株型、产量潜力高、氮肥利用率高的候选骨干亲本。为了更好地了解其高产潜力的遗传基础，我们对KN9204和它的亲本及其衍生品系进行了高通量全基因组重测序（10×）。通过鉴定双亲本定位群体中优良的产量相关数量性状位点（QTL），构建了KN9204的高分辨率遗传组成图谱，显示了有利基因组片段的亲本来源。小偃693是小麦-偃麦草部分双二倍体，对KN9204的高产潜力贡献很大。本研究对来源于小偃693的4个主要稳定QTL进行了精细定位，并阐述了KN9204关键基因组片段在其衍生品系中的的传递，表明含有有益基因组合的单倍型块和育种者的定向选择都是保守的，选择育种在本研究中被证实。本研究为利用分子设计方法育种高产小麦品种提供了理论参考。

Abstract: The foundation parents play key roles in the genetic improvement of both yield potential and end-use quality in wheat. Characterizing the genetic basis that underlies certain beneficial traits in the foundation parents will provide theoretical reference for molecular breeding by a design approach. ‘Kenong 9204’ (KN9204) is a candidate foundation parent characterized by ideotype, high yield potential, and particularly high nitrogen fertilizer utilization. To better understand the genetic basis of its high yield potential, high throughput whole-genome re-sequencing (10×) was performed on KN9204, its parental lines and its derivatives. A high-resolution genetic composition map of KN9204 was constructed, which showed the parental origin of the favorable genomic segments based on the identification of excellent yield-related quantitative trait loci (QTL) from a bi-parental mapping population. Xiaoyan 693 (XY693), a wheat–Thinopyrum ponticum partial amphidiploid, contributed a great deal to the high yield potential of KN9204, and three major stable QTLs from XY693 were fine mapped. The transmissibility of key genomic segments from KN9204 to its derivatives were delineated, indicating that haplotype blocks containing beneficial gene combinations were conserved along with directional selection by breeders. Evidence for selection sweeps in the breeding programs was identified. This study provides a theoretical reference for the breeding of high-yield wheat varieties by a molecular design approach.

Key words: Kenong 9204 , high-yielding potential , quantitative trait locus , genetic composition map , key genomic regions

ZHAO Chun-hua, ZHANG Na, FAN Xiao-li, JI Jun, SHI Xiao-li, CUI Fa, LING Hong-qing, LI Jun-ming. 普通小麦科农9204高产潜力关键区段的解析[J]. Journal of Integrative Agriculture, 2023, 22(9): 2603-2616.

ZHAO Chun-hua, ZHANG Na, FAN Xiao-li, JI Jun, SHI Xiao-li, CUI Fa, LING Hong-qing, LI Jun-ming. Dissecting the key genomic regions underlying high yield potential in common wheat variety ‘Kenong 9204’[J]. Journal of Integrative Agriculture, 2023, 22(9): 2603-2616.

参考文献

Andolfatto P. 2001. Adaptive hitchhiking effects on genome variability. Current Opinion in Genetics & Development, 11, 635–641.

Ceoloni C, Forte P, Kuzmanović L, Tundo S, Moscetti I, Vita P D, Virili M E, D’Ovidio R. 2017. Cytogenetic mapping of a major locus for resistance to Fusarium head blight and crown rot of wheat on Thinopyrum elongatum 7EL and its pyramiding with valuable genes from a Th. ponticum homoeologous arm onto bread wheat 7DL. Theoretical and Applied Genetics, 130, 2005–2024.

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, Appels R, Han D J, Song W N, Sun Q X, et al. 2019. Frequent intra- and inter-species introgression shapes the landscape of genetic variation in bread wheat. Genome Biology, 20, 136.

Cui F, Fan X L, Chen M, Zhang N, Zhao C H, Zhang W, Han J, Ji J, Zhao X Q, Yang L J, Zhao Z W, Tong Y P, Wang T, Li J M. 2016. QTL detection for wheat kernel size and quality and the responses of these traits to low nitrogen. Theoretical and Applied Genetics, 129, 469–484.

Cui F, Fan X L, Zhao C H, Chen M, Ji J, Zhang W, Li J M. 2014. A novel genetic map of wheat: Utility for mapping QTL for yield under different nitrogen treatments. BMC Genetics, 15, 57.

Cui F, Zhang N, Fan X L, Zhang W, Zhao C H, Yang L J, Pan R Q, Chen M, Han J, Zhao X Q, Ji J, Tong Y P, Zhang H X, Jia J Z, Zhao G Y, Li J M. 2017. Utilization of a Wheat660K SNP array-derived high-density genetic map for high-resolution mapping of a major QTL for kernel number. Scientific Reports, 7, 3788.

Cui Z L, Zhang F S, Chen X P, Li F, Tong Y P. 2011. Using in-season nitrogen management and wheat cultivars to improve nitrogen use efficiency. Soil Science Society of America Journal, 75, 976–983.

Deng M, He Y J, Gou L L, Yao F J, Li J, Zhang X M, Long L, Ma J, Jiang Q T, Liu Y X, Wei Y M, Chen G Y. 2018. Genetic effects of key genomic regions controlling yield-related traits in wheat founder parent Fan 6. Acta Agronomica Sinica, 44, 706−715. (in Chinese)

Doebley J F, Gaut B S, Smith B D. 2006. The molecular genetics of crop domestication. Cell, 127, 1309–1321.

Fan X L, Cui F, Ji J, Zhang W, Zhao X Q, Liu J J, Meng D Y, Tong Y P, Wang T, Li J M. 2019. Dissection of pleiotropic QTL regions controlling wheat spike characteristics under different nitrogen treatments using traditional and conditional QTL mapping. Frontiers in Plant Science, 10, 187.

Fan X L, Cui F, Zhao C H, Zhang W, Yang L J, Zhao X Q, Han J, Su Q N, Ji J, Zhao Z W, Tong Y P, Li J M. 2015. QTLs for flag leaf size and their influence on yield-related traits in wheat (Triticum aestivum L.). Molecular Breeding, 24, 35.

Fan X L, Zhang W, Zhang N, Chen M, Zheng S S, Zhao C H, Han J, Liu J J, Zhang X L, Song L Q, Ji J, Liu X G, Ling H Q, Tong Y P, Cui F, Wang T, Li J M. 2018. Identification of QTL regions for seedling root traits and their effect on nitrogen use efficiency in wheat (Triticum aestivum L.). Theoretical and Applied Genetics, 131, 2677–2698.

FAO (Food and Agriculture Organization of the United Nations). 2019. FAO response to global food security challenges. http://www.fao.org/faostat/en/#data/QC

Fradgley N, Gardner K A, Cockram J, Elderfield J, Hickey J M, Howell P, Jackson R, Mackay I J. 2019. A large-scale pedigree resource of wheat reveals evidence for adaptation and selection by breeders. PLoS Biology, 17, e3000071.

Friebe B, Zeller F J, Kunzmann R. 1987. Transfer of the 1BL/1RS wheat-rye-translocation from hexaploid bread wheat to tetraploid durum wheat. Theoretical and Applied Genetics, 74, 423–425.

Gaire R, Ohm H, Brown-Guedira G, Mohammadi M. 2020. Identification of regions under selection and loci controlling agronomic traits in a soft red winter wheat population. Plant Genome, 13, e20031.

Godfray H C J, Beddington J R, Crute I R, Haddad L, Lawrence D, Muir J F, Pretty J, Sherman R, Sandy M T, Camilla T. 2010. Food security: The challenge of feeding 9 billion people. Science, 327, 812–818.

Han J, Zhang L S, Li J T, Shi L J, Xie C J, You M S, Yang Z M, Liu G T, Sun Q X, Liu Z Y. 2009. Molecular dissection of core parental cross “Triumph/Yanda 1817” and its derivatives in wheat breeding program. Acta Agronomica Sinica, 35, 1395–1404. (in Chinese)

Han Z G, Hu Y, Tian Q, Cao Y W, Si A J, Si Z F, Zang Y H, Xu C Y, Shen W J, Dai F, Liu X, Fang L, Chen H, Zhang T Z. 2020. Genomic signatures and candidate genes of lint yield and fiber quality improvement in upland cotton in Xinjiang. Plant Biotechnology Journal, 18, 2002–2014.

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, Maccaferr M, Tuberosa R, Lu H F, Zhang X Y. 2020. Resequencing of 145 landmark cultivars reveals asymmetric sub-genome selection and strong founder genotype effects on wheat breeding in China, Molecular Plant, 13, 1–19.

Holland J B. 2001. Epistasis and plant breeding. In: Janick J, ed., Plant Breeding Reviews. John Wiley and Sons, Greece. pp. 27–92.

Kuzmanovića L, Ruggeri R, Virili M E, Rossini F, Ceoloni C. 2016. Effects of Thinopyrum ponticum chromosome segments transferred into durum wheat on yield components and related morpho-physiological traits in Mediterranean rain-fed conditions. Field Crops Research, 186, 86–98.

Li G R, Zhang T, Yu Z H, Wang H J, Yang E J, Yang Z J. 2021. An efficient Oligo-FISH painting system for revealing chromosome rearrangements and polyploidization in Triticeae. Plant Journal, 105, 978–993.

Li H J, Wang X M. 2009. Thinopyrum ponticum and Th. intermedium: the promising source of resistance to fungal and viral diseases of wheat. Journal of Genetics and Genomics, 36, 557–565.

Lorenzen L L, Boutin S, Young N, Specht J E, Shoemaker R C. 1995. Soybean pedigree analysis using map-based molecular markers: I. Tracking RFLP markers in cultivars. Crop Science, 35, 1326–1336.

Meyer R S, DuVal A E, Jensen H R. 2012. Patterns and processes in crop domestication: An historical review and quantitative analysis of 203 global food crops. New Phytologist, 196, 29–48.

Mohammad M, Donald S. 2019. Sustainable wheat (Triticum aestivum L.) production in saline fields: A review. Critical Reviews in Biotechnology, 39, 999–1014.

Myles S, Peiffer J, Brown P J, Ersoz E S, Zhang Z, Costich D E, Buckler E S. 2009. Association mapping: Critical considerations shift from genotyping to experimental design. Plant Cell, 21, 2194–2202.

Peng J R, Richards D E, Hartley N M, Murphy G P, Devos K M, Flintham J E, Beales J, Fish L J, Worland A J, Pelica F, Sudhakar D, Christou P, Snape J W, Gale M D, Harberd N P. 1999. ‘Green revolution’ genes encode mutant gibberellin response modulators. Nature, 400, 256–261.

Rabinovich S. 1998. Importance of wheat–rye translocations for breeding modern cultivar of Triticum aestivum L. Euphytica, 100, 323–340.

Ray D K, Mueller N D, West P C, Foley J A. 2013. Yield trends are insufficient to double global crop production by 2050. PLoS ONE, 8, e66428.

Ren Y, Chen D, Li W J, Tao L, Yuan G Q, Cao Y, Li X M, Deng Q M, Wang S Q, Zheng A P, Zhu J, Liu H N, Wang L X, Li P, Li S C. 2021. Genome-wide pedigree analysis of elite rice Shuhui 527 reveals key regions for breeding. Journal of Integrative Agriculture, 20, 35–45.

Salvi S, Tuberosa R. 2005. To clone or not to clone plant QTLs: present and future challenges. Trends in Plant Science, 10, 297–304.

Schlötterer C. 2003. Hitchhiking mapping - functional genomics from the population genetics perspective. Trends in Genetics, 19, 32–38.

Shen X, Oh H. 2007. Molecular mapping of Thinopyrum-derived Fusarium head blight resistance in common wheat. Molecular Breeding, 20, 131–140.

Shi X L, Cui F, Han X Y, He Y L, Zhao L, Zhang N, Zhu H D, Liu Z X, Ma B, Zheng S S, Zhang W, Liu J J, Fan X L, Si Y Q, Tian S Q, Niu J Q, Wu H L, Liu X M, Chen Z, Meng D Y, et al. 2022. Comparative genomic and transcriptomic analyses uncover the molecular basis of high nitrogen use efficiency in the wheat cultivar Kenong9204. Molecular Plant, 15, 1440–1456.

Shiferaw B, Smale M, Braun H, Duveiller E, Reynolds M, Muricho G. 2013. Crops that feed the world 10. Past successes and future challenges to the role played by wheat in global food security. Food Security, 5, 291–317.

Si Q L, Liu X L, Liu Z K, Wang C Y, Ji W Q. 2009. SSR analysis of Funo wheat and its derivatives. Acta Agronomica Sinica, 35, 615–619. (in Chinese)

Tong C Y, Yang G T, B A, Li H W, Li B, Li Z S, Zheng Q. 2022. Screening of salt-tolerant Thinopyrum ponticum under two coastal region salinity stress levels. Frontiers in Genetics, 13, 832013.

Varshney R K, Sinha P, Singh V K, Kumar A, Zhang Q F, Bennetzen J L. 2019. 5Gs for crop genetic improvement. Current Opinion in Plant Biology, 13, 190–196.

Wang H W, Sun S L, Ge W Y, Zhao L F, Hou B Q, Wang K, Lyu Z F, Chen L Y, Xu S S, Guo J, Li M, Su P S, Li X F, Wang G P, Bo C Y, Fang X J, Zhuang W W, Cheng X X, Wu J W, Dong L H, et al. 2020. Horizontal gene transfer of Fhb7 from fungus underlies Fusarium head blight resistance in wheat. Science, 368, eaba5435.

Wang R F, An D G, Hu C S, Li L H, Zhang Y M, Jia Y G, Tong Y P. 2011. Relationship between nitrogen uptake and use efficiency of winter wheat grown in the North China Plain. Crop & Pasture Science, 62, 504–514.

Yang G T, Tong C Y, Li H W, Li B, Li Z S, Zhen Q. 2022. Cytogenetic identification and molecular marker development of a novel wheat–Thinopyrum ponticum translocation line with powdery mildew resistance. Theoretical and Applied Genetics, 135, 2041–2057.

Zhang N, Fan X L, Cui F, Zhao C H, Zhang W, Zhao X Q, Yang L J, Pan R Q, Chen M, Han J, Ji J, Liu D C, Zhao Z W, Tong Y P, Zhang A M, Wang T, Li J M. 2017. Characterization of the temporal and spatial expression of wheat (Triticum aestivum L.) plant height at the QTL level and their influence on yield related traits. Theoretical and Applied Genetics, 130, 1235–1252.

Zhao C H, Cui F, Fan Z Q, Gao J R, Wang H G. 2013. Genetic effect analysis of important loci in the backbone parent Aimengniu-derived type V. Australian Journal of Crop Science, 7, 182–188.

Zhuang Q S. 2003, Chinese Wheat Improvement and Pedigree Analysis. China Agricultural Press, Beijing. (in Chinese)

普通小麦科农9204高产潜力关键区段的解析

Dissecting the key genomic regions underlying high yield potential in common wheat variety ‘Kenong 9204’

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