Construction of a high-density adzuki bean genetic map and evaluation of its utility based on a QTL analysis of seed size

doi:10.1016/S2095-3119(20)63343-3

Journal of Integrative Agriculture ›› 2021, Vol. 20 ›› Issue (7): 1753-1761.DOI: 10.1016/S2095-3119(20)63343-3

收稿日期:2019-12-25 出版日期:2021-07-01 发布日期:2021-06-02

Construction of a high-density adzuki bean genetic map and evaluation of its utility based on a QTL analysis of seed size

WANG Li-xia¹, WANG Jie¹, LUO Gao-ling², YUAN Xing-xing³, GONG Dan¹, HU Liang-liang¹, WANG Su-hua¹, CHEN Hong-lin¹, CHEN Xin³, CHENG Xu-zhen¹

¹ Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, P.R.China
² Institute of Rice Research, Guangxi Academy of Agricultural Sciences, Nanning 530007, P.R.China
³ Institute of Economic Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, P.R.China

Received:2019-12-25 Online:2021-07-01 Published:2021-06-02
Contact: Correspondence CHENG Xu-zhen, Tel: +86-10-62189159, E-mail: chengxuzhen@caas.cn
About author:WANG Li-xia, E-mail: wanglixia03@caas.cn
Supported by:
The study was supported by the National Key Research & Development Program of China (2019YFD1001300 and 2019YFD1001303), the earmarked fund for China Agriculture Research System (CARS-08) and the Agricultural Science Technology Innovation Program (ASTIP) of Chinese Academy of Agricultural Sciences.

摘要/Abstract

摘要：

小豆(Vigna angularis (Willd.) Ohwi & Ohashi) 属于豇豆属亚洲豇豆亚属，是东亚各国传统种植作物。小豆营养丰富、医食两用，消费市场逐渐遍布全球。然而，小豆的遗传研究相对缓慢，导致育种技术落后、效率低下，难以满足生产和市场的需求。本研究基于高通量基因组测序技术构建了小豆SNP高密度遗传连锁图谱，该图谱共11条连锁群，含2904个标记，每条连锁群的标记数从208个（LG7）到397（LG1）个不等。图谱总长1365.0cM，标记间平均距离0.47cM，每条连锁群的长度从97.4cM（LG9）到155.6cM（LG1）不等。利用该图谱共发掘到两个与籽粒大小有关的主效QTL，分别位于LG2（22.1%）和LG 9（18.8%）。此外，基于InDel侧翼序列，进一步开发了9718对引物，并随机选择200对进行PCR扩增检验，结果显示有75对在24份小豆种质中具有多态性。本研究中高密度图谱构建及籽粒大小的QTL 分析将进一步提升小豆重要性状基因的发掘等，而InDel标记的开发将有效促进小豆种质资源的遗传多样性分析、基因初步定位等研究。

Abstract:

Adzuki bean (Vigna angularis (Willd.) Ohwi & Ohashi) is an annual cultivated leguminous crop commonly grown in Asia and consumed worldwide. However, there has been limited research regarding adzuki bean genetics, which has prevented the efficient application of genes during breeding. In the present study, we constructed a high-density genetic map based on whole genome re-sequencing technology and validated its utility by mining QTLs related to seed size. Moreover, we analyzed the sequences flanking insertions/deletions (InDels) to develop a set of PCR-based markers useful for characterizing adzuki bean genetics. A total of 2 904 markers were mapped to 11 linkage groups (LGs). The total length of the map was 1 365.0 cM, with an average distance between markers of 0.47 cM. Among the LGs, the number of markers ranged from 208 (LG7) to 397 (LG1) and the total distance ranged from 97.4 cM (LG9) to 155.6 cM (LG1). Twelve QTLs related to seed size were identified using the constructed map. The two major QTLs in LG2 and LG9 explained 22.1 and 18.8% of the total phenotypic variation, respectively. Ten minor QTLs in LG4, LG5 and LG6 explained 3.0–10.4% of the total phenotypic variation. A total of 9 718 primer pairs were designed based on the sequences flanking InDels. Among the 200 selected primer pairs, 75 revealed polymorphisms in 24 adzuki bean germplasms. The genetic map constructed in this study will be useful for screening genes related to other traits. Furthermore, the QTL analysis of seed size and the novel markers described herein may be relevant for future molecular investigations of adzuki bean and will be useful for exploiting the mechanisms underlying legume seed development.

Key words: Vigna angularis , genetic map , QTL , seed size , PCR-based marker development

. [J]. Journal of Integrative Agriculture, 2021, 20(7): 1753-1761.

WANG Li-xia, WANG Jie, LUO Gao-ling, YUAN Xing-xing, GONG Dan, HU Liang-liang, WANG Su-hua, CHEN Hong-lin, CHEN Xin, CHENG Xu-zhen. Construction of a high-density adzuki bean genetic map and evaluation of its utility based on a QTL analysis of seed size[J]. Journal of Integrative Agriculture, 2021, 20(7): 1753-1761.

参考文献

Ayana A, Bekele E, Bryngelsson T. 2000. Genetic variation in wild sorghum (Sorghum bicolor ssp. verticilliflorum (L.) Moench) germplasm from Ethiopia assessed by random amplified polymorphic DNA (RAPD). Hereditas, 132, 249–254.
Das S, Upadhyaya H D, Srivastava R, Bajaj D, Gowda C L, Sharma S, Singh S, Tyagi A K, Parida S K. 2015. Genome-wide insertion-deletion (InDel) marker discovery and genotyping for genomics-assisted breeding applications in chickpea. DNA Research, 22, 377–386.
Elshire R J, Glaubitz J C, Sun Q, Poland J A, Kawamoto K, Buckler E S, Mitchell S E. 2011. A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS ONE, 6, e19379.
Han O K, Kaga A, Isemura T, Wang X W, Tomooka N, Vaughan D A. 2005. A genetic linkage map for azuki bean (Vigna angularis (Willd.) Ohwi & Ohashi). Theoretical and Applied Genetics, 111, 1278–1287.
Isemura T, Kaga A, Konishi S, Ando T, Tomooka N, Han O K, Vaughan D A. 2007. Genome dissection of traits related to domestication in azuki bean (Vigna angularis) and comparison with other warm-season legumes. Annals of Botany, 100, 1053–1071.
Isemura T, Tomooka N, Kaga A, Vaughan D A. 2011. Comparison of the pattern of crop domestication between two Asian beans, azuki bean (Vigna angularis) and rice bean (V. umbellata). Japan Agricultural Research Quarterly, 45, 23–30.
Jin W L, Pu S J, Zhao B, Li S L. 2006. Genetic variation of 100-seed weight and size of starch granules in adzuki bean germplasm resource groups. Acta Agriculturae Boreali-Sinica, 21, 41–44. (in Chinese)
Kaga A, Isemura T, Tomooka N, Vaughan D A. 2008. The genetics of domestication of the azuki bean (Vigna angularis). Genetics, 178, 1013–1036.
Kaga A, Ohnishi M, Ishii T, Kamijima O. 1996. A genetic linkage map of azuki bean constructed with molecular and morphological markers using an interspecific population (Vigna angularis×V. nakashimae). Theoretical and Applied Genetics, 93, 658–663.
Kang Y J, Satyawan D, Shim S, Lee T, Lee J, Hwang W J, Kim S K, Lestari P, Laosatit K, Kim K H. 2015. Draft genome sequence of adzuki bean, Vigna angularis. Scientific Reports, 5, 8069.
Li H, Durbin R. 2009. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics, 25, 1754–1760.
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R. 2009. The sequence alignment/map format and SAM tools. Bioinformatics, 25, 2078–2079.
Li H, Ye G, Wang J. 2007. A modified algorithm for the improvement of composite interval mapping. Genetics, 175, 361–374.
Li W, Cheng J, Wu Z, Qin C, Tan S, Tang X, Cui J, Zhang L, Hu K. 2015. An InDel-based linkage map of hot pepper (Capsicum annuum). Molecular Breeding, 35, 32.
Li Y, Yang K, Yang W, Chu L, Chen C, Zhao B, Li Y, Jian J, Yin Z, Wang T, Wan P. 2017. Identification of QTL and qualitative trait loci for agronomic traits using SNP markers in the adzuki bean. Frontiers in Plant Science, 8, 840.
Liu C, Fan B, Cao Z, Su Q, Wang Y, Zhang Z, Tian J. 2016. Development of a high-density genetic linkage map and identification of flowering time QTLs in adzuki bean (Vigna angularis). Scientific Reports, 6, 39523.
Luo W X, Zhang L, Yang K, Li Y S, Zhao B, Li M, Wan P. 2013. Construction of genetic linkage map using SSR molecular markers in azuki bean (Vigna angularis Ohwi & Ohashi). Scientia Agricultura Sinica, 46, 3534–3544. (in Chinese)
McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, DePristo M A. 2010. The genome analysis toolkit: A map reduce framework for analyzing next-generation DNA sequencing data. Genome Research, 20, 1297–1303.
Mills R E, Luttig C T, Larkins C E, Beauchamp A, Tsui C, Pittard W S, Devine S E. 2006. An initial map of insertion and deletion (INDEL) variation in the human genome. Genome Research, 16, 1182–1190.
Moghaddam S M, Song Q, Mamidi S, Schmutz J, Lee R, Cregan P, Osorno J M, McClean P E. 2014. Developing market class specific InDel markers from next generation sequence data in Phaseolus vulgaris L. Frontiers in Plant Science, 5, 185.
Ren D, Wang X, Yang M, Yang L, He G, Deng X W. 2019. A new regulater of seed size control in Arabidopsis indentified by a genome-wide association study. New Phytologist, 222, 895–906.
Rozen S, Skaletsky H. 2000. Primer3 on the WWW for general users and for biologist programmers. Methods in Molecular Biology, 132, 365–386.
Sakai H, Naito K, Takahashi Y, Sato T, Yamamoto T, Muto I, Itoh T, Tomooka N. 2016. The Vigna genome server, “VigGS”: A genomic knowledge base of the genus Vigna based on high-quality, annotated genome sequence of the azuki bean, Vigna angularis (Willd.) Ohwi & Ohashi. Plant and Cell Physiology, 57, e2.
Sun X, Liu D, Zhang X, Li W, Liu H, Hong W, Jiang C, Guan N, Ma C, Zeng H, Xu C, Song J, Huang L, Wang C, Shi J, Wang R, Zheng X, Lu C, Wang X, Zheng H. 2013. SLAF-seq: An efficient method of large-scale de novo SNP discovery and genotyping using high-throughput sequencing. PLoS ONE, 8, e58700.
Tomooka N, Vaughan D A, Moss H, Maxted N. 2003. The Asian Vigna: The Genus Vigna Sugenus Ceratotropis Genetic Resource. KIuwer Academic Publishers, London.
Wang L X, Cheng X Z, Wang S H, Liang H, Zhao D, Xu N. 2009. Genetic diversity of adzuki bean germplasm resources revealled by SSR markers. Acta Agronomica Sinica, 35, 1858–1865. (in Chinese)
Wang L X, Cheng X Z, Wang S H, Tian J. 2012. Analysis of an applied core collection of adzuki bean germplasm by using SSR markers. Journal of Integrative Agriculture, 11, 1601–1609.
Xu L Y, Wang L Y, Wei K, Tan L Q, Su J J, Cheng H. 2018. High-density SNP linkage map construction and QTL mapping for flavonoid-related traits in a tea plant (Camellia sinensis) using 2b-RAD sequencing. BMC Genomics, 19, 955.
Yang K, Tian Z, Chen C, Luo L, Zhao B, Wang Z, Yu L, Li Y, Sun Y, Li W, Chen Y, Li Y, Zhang Y, Ai D, Zhao J, Shang C, Ma Y, Wu B, Wang M, Gao L, et al. 2015. Genome sequencing of adzuki bean (Vigna angularis) provides insight into high starch and low fat accumulation and domestication. Proceedings of the National Academy of Sciences of the United States of America, 112, 13213–13218.
Yao Y, Cheng X, Wang L, Wang S, Ren G. 2011. A determination of potential alpha-glucosidase inhibitors from Azuki beans (Vigna angularis). International Journal of Molecular Sciences, 12, 6445–6451.
Zhou G, Zhang Q, Tan C, Zhang X Q, Li C. 2015. Development of genome-wide InDel markers and their integration with SSR, DArT and SNP markers in single barley map. BMC Genomics, 16, 804.

Construction of a high-density adzuki bean genetic map and evaluation of its utility based on a QTL analysis of seed size

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