花生株高与分枝相关性状QTL分析

doi:10.1016/j.jia.2023.12.009

摘要/Abstract

摘要：

株高、侧枝长和分枝数是影响花生株型的关键组分性状，对花生的生物量、荚果产量以及机械化作业适配性至关重要。本研究利用包含181个家系的重组自交系群体，开展了3个环境下的表型考察，发现株高、侧枝长和分枝数均表现为连续分布和超亲遗传，其广义遗传率分别为0.87、0.88和0.92。基于单环境非条件QTL分析，共检测到35个加性QTL，表型贡献率为4.57%~21.68%。通过两轮meta分析将以上加性QTL整合为24个一致性（consensus）位点和17个特异性（unique）位点，其中5个特异性位点表现为多效性。利用条件QTL分析阐明了多效性位点的遗传基础（‘多基因连锁’或者‘一因多效’）。此外，基于多环境联合分析估算了加性QTL与环境的互作效应，互作效应对株高、侧枝长和分枝数的总贡献率分别达到10.80%，11.02%和7.89%。本研究在第9、10和16染色体上鉴定到3个稳定主效特异性QTL区段（uq9-3、uq10-2 和uq16-1），物理区间范围为1.43-1.53Mb，其中参与植物激素合成、信号转导和细胞壁发育的一些基因可能是调控这些性状的候选基因。该研究结果为后续花生株型遗传研究和分子标记辅助育种提供了重要基础。

Abstract:

Plant height (PH), primary lateral branch length (PBL) and branch number (BN) are architectural components impacting peanut pod yield, biomass production and adaptivity to mechanical harvesting. In this study, a recombinant inbred population consisting of 181 individual lines was used to determine genetic controls of PH, PBL and BN across three environments. Phenotypic data collected from the population demonstrated continuous distributions and transgressive segregation patterns. Broad-sense heritability of PH, PBL and BN was found to be 0.87, 0.88 and 0.92, respectively. Unconditional individual environmental analysis revealed 35 additive QTLs with phenotypic variation explained (PVE) ranging from 4.57 to 21.68%. A two-round meta-analysis resulted in 24 consensus and 17 unique QTLs. Five unique QTLs exhibited pleiotropic effects and their genetic bases (pleiotropy or tight linkage) were evaluated. Joint analysis was performed to estimate the QTL by environment interaction (QEI) effects on PH, PBL and BN, which collectively explained phenotypic variations of 10.80, 11.02, and 7.89%, respectively. We identified 3 major and stable QTL regions (uq9-3, uq10-2 and uq16-1) on chromosomes 9, 10 and 16, spanning 1.43-1.53 Mb genomic regions. Candidate genes involved in phytohormones biosynthesis, signaling and cell wall development were proposed to regulate these morphological traits. These results provide valuable information for further genetic studies and development of molecular markers applicable for peanut architecture improvement.

Key words: peanut , plant height , , branching , , QTL mapping , , candidate gene

. 花生株高与分枝相关性状QTL分析[J]. Journal of Integrative Agriculture, DOI: 10.1016/j.jia.2023.12.009.

ZHANG Sheng-zhong, HU Xiao-hui, WANG Fei-fei, MIAO Hua-rong, Ye Chu, YANG Wei-qiang, ZHONG Wen, CHEN Jing. Identification of QTLs for plant height and branching related traits in cultivated peanut[J]. Journal of Integrative Agriculture, DOI: 10.1016/j.jia.2023.12.009.

参考文献

Ashikari M, Sakakibara H, Lin S, Yamamoto T, Takashi T, Nishimura A, Angeles E R, Qian Q, Kitano H, Mastuoka M. 2005. Cytokinin oxidase regulates rice grain production. Science, 309, 741–745.

Benkova E, Michniewicz M, Sauer M, Teichmann T, Seifertova D, Jürgens G, Friml J. 2003. Local, efflux-dependent auxin gradients as a common module for plant organ formation. Cell, 115, 591–602.

Bertioli D J, Jenkins J, Clevenger J, Dudchenko O, Gao D, Seijo G, Leal-Bertioli S C M, Ren L, Farmer A D, Pandey M K, Samoluk S S, Abernathy B, Agarwal G, Ballén-Taborda C, Cameron C, Campbell J, Chavarro C, Chitikineni A, Chu Y, Dash S, et al. 2019. The genome sequence of segmental allotetraploid peanut Arachis hypogaea. Nature Genetics, 51, 877–884.

Clevenger J, Chu Y, Scheffler B, Ozias-Akins P. 2016. A developmental transcriptome map for allotetraploid Arachis hypogaea. Frontiers in Plant Science, 7, 1446.

Fang Y, Zhang X, Liu H, Wu J, Qi F, Sun Z, Zheng Z, Dong W, Huang B. 2023. Identification of quantitative trait loci and development of diagnostic markers for growth habit traits in peanut (Arachis hypogaea L.). Theoretical and Applied Genetics, 136, 105.

Fonceka D, Tossim H A, Rivallan R, Vignes H, Lacut E, de Bellis F, Faye I, Ndoye O, Leal-Bertioli S C, Valls J F, Bertioli D J, Glaszmann J C, Courtois B, Rami J F. 2012. Construction of chromosome segment substitution lines in peanut (Arachis hypogaea L.) using a wild synthetic and QTL mapping for plant morphology. PLoS ONE, 7, e48642.

Hake A A, Shirasawa K, Yadawad A, Sukruth M, Patil M, Nayak S N, Lingaraju S, Patil P V, Nadaf H L, Gowda M V C, Bhat R S. 2017. Mapping of important taxonomic and productivity traits using genic and non-genic transposable element markers in peanut (Arachis hypogaea L.). PLoS ONE, 12, e0186113.

Hill W G, Zhang X S. 2012. On the pleiotropic structure of the genotype-phenotype map and the evolvability of complex organisms. Genetics, 190, 1131–1137.

Huang L, He H, Chen W, Ren X, Chen Y, Zhou X, Xia Y, Wang X, Jiang X, Liao B, Jiang H. 2015. Quantitative trait locus analysis of agronomic and quality-related traits in cultivated peanut (Arachis hypogaea L.). Theoretical and Applied Genetics, 128, 1103–1115.

Huang L, Ren X, Wu B, Li X, Chen W, Zhou X, Chen Y, Pandey M K, Jiao Y, Luo H, Lei Y, Varshney R K, Liao B, Jiang H. 2016. Development and deployment of a high-density linkage map identified quantitative trait loci for plant height in peanut (Arachis hypogaea L.). Scientific Reports, 6, 39478.

Jiang H, Huang L, Ren X, Chen Y, Zhou X, Xia Y, Huang J, Lei Y, Yan L, Wan L, Liao B. 2014. Diversity characterization and association analysis of agronomic traits in a Chinese peanut (Arachis hypogaea L.) mini-core collection. Journal of Integrative Plant Biology, 56, 159–169.

Lenhard M, Laux T. 2003. Stem cell homeostasis in the Arabidopsis shoot meristem is regulated by intercellular movement of CLAVATA3 and its sequestration by CLAVATA1. Development, 130, 3163–3173.

Li L, Yang X, Cui S, Meng X, Mu G, Hou M, He M, Zhang H, Liu L, Chen C Y. 2019. Construction of high-density genetic map and mapping quantitative trait loci for growth habit-related traits of peanut (Arachis hypogaea L.). Frontiers in Plant Science, 10, 745.

Li M, Tang D, Wang K, Wu X, Lu L, Yu H, Gu M, Yan C, Cheng Z. 2011. Mutations in the F-box gene LARGER PANICLE improve the panicle architecture and enhance the grain yield in rice. Plant Biotechnology Journal, 9, 1002–1013.

Li Y, Li L, Zhang X, Zhang K, Ma D, Liu J, Wang X, Liu F, Wan Y. 2017. QTL mapping and marker analysis of main stem height and the first lateral branch length in peanut (Arachis hypogaea L.). Euphytica, 213, 57.

Liao Z, Yu H, Duan J, Yuan K, Yu C, Meng X, Kou L, Chen M, Jing Y, Liu G, Smith S M, Li J. 2019. SLR1 inhibits MOC1 degradation to coordinate tiller number and plant height in rice. Nature Communications, 10, 2738.

Lv J, Liu N, Guo J, Xu Z, Li X, Li Z, Luo H, Ren X, Huang L, Zhou X, Chen Y, Chen W, Lei Y, Tu J, Jiang H, Liao B. 2018. Stable QTLs for plant height on chromosome A09 identified from two mapping populations in peanut (Arachis hypogaea L.). Frontiers in Plant Science, 9, 684.

Mackay I J, Cockram J, Howell P, Powell W. 2021. Understanding the classics: The unifying concepts of transgressive segregation, inbreeding depression and heterosis and their central relevance for crop breeding. Plant Biotechnology Journal, 19, 26–34.

Mammadov J, Aggarwal R, Buyyarapu R, Kumpatla S. 2012. SNP markers and their impact on plant breeding. International Journal of Plant Genomics, 2012, 728398.

Meng L, Li H, Zhang L, Wang J. 2015. QTL IciMapping: Integrated software for genetic linkage map construction and quantitative trait locus mapping in biparental populations. The Crop Journal, 3, 269–283.

Reintanz B, Lehnen M, Reichelt M, Gershenzon J, Kowalczyk M, Sandberg G, Godde M, Uhl R, Palme K. 2001. bus, a bushy Arabidopsis CYP79F1 knockout mutant with abolished synthesis of short-chain aliphatic glucosinolates. The Plant Cell, 13, 351–367.

Schoof H, Lenhard M, Haecker A, Mayer K F, Jurgens G, Laux T. 2000. The stem cell population of Arabidopsis shoot meristems is maintained by a regulatory loop between the CLAVATA and WUSCHEL genes. Cell, 100, 635–644.

Shen Y, Xiang Y, Xu E, Ge X, Li Z. 2018. Major co-localized QTL for plant height, branch initiation height, stem diameter, and flowering time in an alien introgression derived Brassica napus DH population. Frontiers in Plant Science, 9, 390.

Sheng P, Wu F, Tan J, Zhang H, Ma W, Chen L, Wang J, Wang J, Zhu S, Guo X, Wang J, Zhang X, Cheng Z, Bao Y, Wu C, Liu X, Wan J. 2017. A CONSTANS-like transcriptional activator, OsCOL13, functions as a negative regulator of flowering downstream of OsphyB and upstream of Ehd1 in rice. Plant Molecular Biology, 92, 209–222.

Shirasawa K, Koilkonda P, Aoki K, Hirakawa H, Tabata S, Watanabe M, Hasegawa M, Kiyoshima H, Suzuki S, Kuwata C, Naito Y, Kuboyama T, Nakaya A, Sasamoto S, Watanabe A, Kato M, Kawashima K, Kishida Y, Kohara M, Kurabayashi A, et al. 2012. In silico polymorphism analysis for the development of simple sequence repeat and transposon markers and construction of linkage map in cultivated peanut. BMC Plant Biology, 12, 80.

Sigalas P P, Buchner P, Thomas S G, Jamois F, Arkoun M, Yvin J C, Bennett M J, Hawkesford M J. 2023. Nutritional and tissue-specific regulation of cytochrome P450 CYP711A MAX1 homologues and strigolactone biosynthesis in wheat. Journal of Experimental Botany, 74, 1890–1910.

Song Y, You J, Xiong L. 2009. Characterization of OsIAA1 gene, a member of rice Aux/IAA family involved in auxin and brassinosteroid hormone responses and plant morphogenesis. Plant Molecular Biology, 70, 297–309.

Sosnowski O, Charcosset A, Joets J. 2012. BioMercator V3: An upgrade of genetic map compilation and quantitative trait loci meta-analysis algorithms. Bioinformatics, 28, 2082–2083.

Spielmeyer W, Ellis M H, Chandler P M. 2002. Semidwarf (sd-1), “green revolution” rice, contains a defective gibberellin 20-oxidase gene. Proceedings of the National Academy of Sciences of the United States of America, 99, 9043–9048.

Su S, Hong J, Chen X, Zhang C, Chen M, Luo Z, Chang S, Bai S, Liang W, Liu Q, Zhang D. 2021. Gibberellins orchestrate panicle architecture mediated by DELLA–KNOX signaling in rice. Plant Biotechnology Journal, 19, 2304–2318.

Tanabe S, Ashikari M, Fujioka S, Takatsuto S, Yoshida S, Yano M, Yoshimura A, Kitano H, Matsuoka M, Fujisawa Y, Kato H, Iwasaki Y. 2005. A novel cytochrome P450 is implicated in brassinosteroid biosynthesis via the characterization of a rice dwarf mutant, dwarf11, with reduced seed length. The Plant Cell, 17, 776–790.

Tang J, Tian X, Mei E, He M, Gao J, Yu J, Xu M, Liu J, Song L, Li X, Wang Z, Guan Q, Zhao Z, Wang C, Bu Q. 2022. WRKY53 negatively regulates rice cold tolerance at the booting stage by fine-tuning anther gibberellin levels. The Plant Cell, 34, 4495-4515.

Todaka D, Nakashima K, Maruyama K, Kidokoro S, Osakabe Y, Ito Y, Matsukura S, Fujita Y, Yoshiwara K, Ohme-Takagi M, Kojima M, Sakakibara H, Shinozaki K, Yamaguchi-Shinozaki K. 2012. Rice phytochrome-interacting factor-like protein OsPIL1 functions as a key regulator of internode elongation and induces a morphological response to drought stress. Proceedings of the National Academy of Sciences of the United States of America, 109, 15947–15952.

Voorrips R E. 2002. MapChart: Software for the graphical presentation of linkage maps and QTLs. Journal of Heredity, 93, 77–78.

Wagner G P, Zhang J. 2011. The pleiotropic structure of the genotype–phenotype map: The evolvability of complex organisms. Nature Reviews Genetics, 12, 204–213.

Wang D, Qin B, Li X, Tang D, Zhang Y, Cheng Z, Xue Y. 2016a. Nucleolar DEAD-box RNA helicase TOGR1 regulates thermotolerant growth as a pre-rRNA chaperone in rice. Plos Genetics, 12, e1005844.

Wang D, Qin Y, Fang J, Yuan S, Peng L, Zhao J, Li X. 2016b. A missense mutation in the zinc finger domain of OsCESA7 deleteriously affects cellulose biosynthesis and plant growth in rice. PLoS ONE, 11, e0153993.

Wang L, Yang X, Cui S, Mu G, Sun X, Liu L, Li Z. 2019. QTL mapping and QTL × environment interaction analysis of multi-seed pod in cultivated peanut (Arachis hypogaea L.). The Crop Journal, 7, 249–260.

Wang S, Basten C J, Zeng Z. 2012. Windows QTL cartographer 2.5. Department of Statistics, North Carolina State University, Raleigh, NC. [2017-08-11]. http://statgen.ncsu. edu/qtlcart/WQTLCart.htm

Wang X, Liang Y, Li L, Gong C, Wang H, Huang X, Li S, Deng Q, Zhu J, Zheng A, Li P, Wang S. 2015. Identification and cloning of tillering-related genes OsMAX1 in rice. Rice Science, 22, 255-263.

Wang Y, Li J. 2008. Molecular basis of plant architecture. Annual Review of Plant Biology, 59, 253–279.

Wang Z, Huai D, Zhang Z, Cheng K, Kang Y, Wan L, Yan L, Jiang H, Lei Y, Liao B. 2018. Development of a high-density genetic map based on specific length amplified fragment sequencing and its application in quantitative trait loci analysis for yield-related traits in cultivated peanut. Frontiers in Plant Science, 9, 827.

Würschum T, Langer S M, Longin C F H. 2015. Genetic control of plant height in European winter wheat cultivars. Theoretical and Applied Genetics, 128, 865–874.

Yamamoto Y, Kamiya N, Morinaka Y, Matsuoka M, Sazuka T. 2007. Auxin biosynthesis by the YUCCA genes in rice. Plant Physiology, 143, 1362–1371.

Yang Y, Hu Y, Li P, Hancock J T, Hu X. 2023. Research progress and application of plant branching. Phyton-International Journal of Experimental Botany, 92, 679–689.

Yin D M, Shang M Z, Cui D Q. 2006. Studies on genetic analysis of major agronomic characters in peanut. Chinese Agriculture Science Bulletin, 22, 261–265. (in Chinese)

Zhang H, Chen J, Li R, Deng Z, Zhang K, Liu B, Tian J. 2016. Conditional QTL mapping of three yield components in common wheat (Triticum aestivum L.). The Crop Journal, 4, 220–228.

Zhang S, Hu X, Miao H, Chu Y, Cui F, Yang W, Wang C, Shen Y, Xu T, Zhao L, Zhang J, Chen J. 2019. QTL identification for seed weight and size based on a high-density SLAF-seq genetic map in peanut (Arachis hypogaea L.). BMC Plant Biology, 19, 537.

Zhang S, Hu X, Wang F, Chu Y, Yang W, Xu S, Wang S, Wu L, Yu H, Miao H, Fu C, Chen J. 2023. A stable and major QTL region on chromosome 2 conditions pod shape in cultivated peanut (Arachis hyopgaea L.). Journal of Integrative Agriculture, 22, 2323–2334.

Zhang S, Wu T, Liu S, Liu X, Jiang L, Wan J. 2016. Disruption of OsARF19 is critical for floral organ development and plant architecture in rice (Oryza sativa L.). Plant Molecular Biology Reporter, 34, 748–760.

Zhu D, Liu Y, Jin M, Chen G, Prodanvovic S, Yan Y. 2019. Expression and function analysis of wheat expasin genes EXPA2 and EXPB1. Genetika, 51, 261–274.