Please wait a minute...
Journal of Integrative Agriculture  2023, Vol. 22 Issue (9): 2648-2659    DOI: 10.1016/j.jia.2023.01.003
Crop Science Advanced Online Publication | Current Issue | Archive | Adv Search |
Construction of SNP genetic maps based on targeted next-generation sequencing and QTL mapping of vital agronomic traits in faba bean (Vicia faba L.)

LI Meng-wei1*, HE Yu-hua2*, LIU Rong1, LI Guan1, WANG Dong1, JI Yi-shan1, YAN Xin1, HUANG Shu-xian1, WANG Chen-yu1, MA Yu3, LIU Bei4, YANG Tao1#, ZONG Xu-xiao1#

1 National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, P.R.China
2 Institute of Grain Crops, Yunnan Academy of Agricultural Sciences, Kunming 650205, P.R.China
3 Department of Horticulture, Washington State University, Pullman, WA 99164, USA
4 China Golden Marker (Beijing) Biotech Co., Ltd., Beijing 102200, P.R.China
Download:  PDF in ScienceDirect  
Export:  BibTeX | EndNote (RIS)      

蚕豆(Vicia faba L.)基因组较大(约13 Gb),尚无参考基因组,与其他豆类相比,蚕豆遗传研究落后很多鉴于此,本研究选择三个蚕豆纯系(云豆8137H0003712H000572)作为亲本构建了两个F2群体,其中群体1云豆8137×H0003712)包含167个单群体2H000572×云豆8137)包含204个单株利用Targeted next-generation sequencingTNGS基因分型平台对两个F2群体进行基因分型,构建了两个高密度的蚕豆SNP遗传连锁图谱基于群体1构建的图谱包含5103SNP标记,长度1333.31 cM,平均标记密度0.26 cM基于群体2构建的图谱包含1904SNP标记覆盖长度1610.61 cM利用上述两个遗传连锁图谱及两个F2群体,挖掘了与蚕豆花、荚、株型和籽粒相关的14个农艺性状的98QTLs此外,本研究对上述两个遗传连锁图谱进行整合,构建了一张包含6895SNP标记,覆盖长度3324.48 cM的整合图谱。本研究不仅为蚕豆相关基因的图位克隆奠定了基础,有助于推动蚕豆分子标记辅助育种的发展

Abstract  Owing to the limitation of a large genome size (~13 Gb), the genetic and gene mapping studies on faba bean (Vicia faba L.) are lagging far behind those for other legumes.  In this study, we selected three purified faba bean lines (Yundou 8137, H0003712, and H000572) as parents and constructed two F2 populations.  These two F2 populations, namely 167 F2 plants in Pop1 (Yundou 8137×H0003712) and 204 F2 plants in Pop2 (H000572×Yundou 8137), were genotyped using a targeted next-generation sequencing (TNGS) genotyping platform, and two high-density single nucleotide polymorphisms (SNP) genetic linkage maps of faba bean were constructed.  The map constructed from Pop1 contained 5 103 SNPs with a length of 1 333.31 cM and an average marker density of 0.26 cM.  The map constructed from Pop2 contained 1 904 SNPs with a greater length of 1 610.61 cM.  In these two F2 populations, QTL mapping identified 98 QTLs for 14 agronomic traits related to the flowers, pods, plant types and grains.  The two maps were then merged into an integrated genetic linkage map containing 6 895 SNPs, with a length of 3 324.48 cM.  These results not only lay the foundation for fine mapping and map-based cloning of related genes, but can also accelerate the molecular marker-assisted breeding of faba bean.
Keywords:  faba bean       targeted next-generation sequencing        single nucleotide polymorphisms        genetic linkage map        QTL mapping  
Received: 17 August 2022   Accepted: 28 October 2022
Fund: This study was supported by the National Key R&D Program of China (2019YFD1001300 and 2019YFD1001303), the Construction of Molecular Database of Faba Bean and Pea and Identification of Maize Germplasm Project, Ministry of Agriculture and Rural Affairs, China (19200030), the Yunnan Key R&D Program, China (202202AE090003), the earmarked fund for China Agriculture Research System (CARS-08), the Crop Germplasm Resources Protection (2130135) and the Major Agricultural Science and Technology Program of Chinese Academy of Agricultural Sciences (CAAS-XTCX20190025).
About author:  #Correspondence YANG Tao, E-mail:; ZONG Xu-xiao, Tel/Fax: +86-10-62186651, E-mail: * These authors contributed equally to this study.

Cite this article: 

LI Meng-wei, HE Yu-hua, LIU Rong, LI Guan, WANG Dong, JI Yi-shan, YAN Xin, HUANG Shu-xian, WANG Chen-yu, MA Yu, LIU Bei, YANG Tao, ZONG Xu-xiao. 2023. Construction of SNP genetic maps based on targeted next-generation sequencing and QTL mapping of vital agronomic traits in faba bean (Vicia faba L.). Journal of Integrative Agriculture, 22(9): 2648-2659.

Alghamdi S S, Migdadi H M, Ammar M H, Paull J G, Siddique K H M. 2012. Faba bean genomics: Current status and future prospects. Euphytica186, 609–624.

Arbaoui M, Link W, Satovic Z, Torres A M. 2008. Quantitative trait loci of frost tolerance and physiologically related trait in faba bean (Vicia faba L.). Euphytica164, 93–104.

Atieno J, Colmer T D, Taylor J, Li Y, Quealy J, Kotula L, Nicol D, Nguyen D T, Brien C, Langridge P, Croser J, Hayes J E, Sutton T. 2021. Novel salinity tolerance loci in chickpea identified in glasshouse and field environments. Frontiers in Plant Science28, 12.

Avila C M, Ruiz-Rodríguez M D, Cruz-Izquierdo S, Atienza S G, Cubero J I, Torres A M. 2017. Identification of plant architecture and yield-related QTL in Vicia faba L. Molecular Breeding37, 88.

Avila C M, Satovic Z, Sillero J C, Nadal S, Rubiales D, Moreno M T, Torres A M. 2005. QTL detection for agronomic traits in faba bean (Vicia faba L.). Agriculturae Conspectus Scientificus70, 65–73.

Avila C M, Satovic Z, Sillero J C, Rubiales D, Moreno M T, Torres A M. 2004. Isolate and organ-specific QTLs for ascochyta blight resistance in faba bean (Vicia faba L). Theoretical and Applied Genetics108, 1071–1078.

Benayad A, Taghouti M, Benali A, Aboussaleh Y, Benbrahim N. 2021. Nutritional and technological assessment of durum wheat-faba bean enriched flours, and sensory quality of developed composite bread. Saudi Journal of Biological Sciences28, 635–642.

Björnsdotter E, Nadzieja M, Chang W, Escobar-Herrera L, Mancinotti D, Angra D, Xia X, Tacke R, Khazaei H, Crocoll C, Vandenberg A, Link W, Stoddard F L, O’Sullivan D M, Stougaard J, Schulman A H, Andersen S U, Geu-Flores F. 2021. VC1 catalyses a key step in the biosynthesis of vicine in faba bean. Nature Plants7, 923–931.

Carrillo-Perdomo E, Vidal A, Kreplak J, Duborjal H, Leveugle M, Duarte J, Desmetz C, Deulvot C, Raffiot B, Marget P, Tayeh N, Pichon J P, Falque M, Martin O C, Burstin J, Aubert G. 2020. Development of new genetic resources for faba bean (Vicia faba L.) breeding through the discovery of gene-based SNP markers and the construction of a high-density consensus map. Scientific Reports10, 6790.

Catt S C, Braich S, Kaur S, Paull J G. 2017. QTL detection for flowering time in faba bean and the responses to ambient temperature and photoperiod. Euphytica213, 125.

Cooper J W, Wilson M H, Derks M F L, Smit S, Kunert K J, Cullis C, Foyer C H. 2017. Enhancing faba bean (Vicia faba L.) genome resources. Journal of Experimental Botany68, 1941–1953.

Cruz-Izquierdo S, Avila C M, Satovic Z, Palomino C, Gutierrez N, Ellwood S R, Phan H T, Cubero J I, Torres A M. 2012. Comparative genomics to bridge Vicia faba with model and closely-related legume species: stability of QTLs for flowering and yield-related traits. Theoretical and Applied Genetics125, 1767–1782.

Díaz-Ruiz R, Torres A M, Satovic Z, Gutierrez M V, Cubero J I, Román B. 2010. Validation of QTLs for Orobanche crenata resistance in faba bean (Vicia faba L.) across environments and generations. Theoretical and Applied Genetics120, 909–919.

Doyle J J, Doyle J L. 1987. A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochemical Bulletin19, 11–15.

Elattar M A, Karikari B, Li S, Song S, Cao Y, Aslam M, Hina A, Abou-Elwafa S F, Zhao T. 2021. Identification and validation of major QTLs, epistatic interactions, and candidate genes for soybean seed shape and weight using two related RIL populations. Frontiers in Genetics12, 666440.

Etemadi F, Hashemi M, Barker A V, Zandvakili O R, Liu X B. 2019. Agronomy, nutritional value, and medicinal application of faba bean (Vicia faba L.). Horticultural Plant Journal5, 170–182.

FAO (Food and Agriculture Organization). 2022. Online statistical database: Crops and livestock products. FAOSTAT. [2022-02-17].

Guo Z F, Wang H W , Tao J J, Ren, Y H, Xu C, Wu K S, Zou C, Zhang J N, Xu Y B. 2019. Development of multiple SNP marker panels affordable to breeders through genotyping by target sequencing (GBTS) in maize. Molecular Breeding39, 37.

Hanelt P. 1972. Die infraspezifische variabilitat von Vicia faba L. und ihre gliederung. Kulturpflanze20, 75–128. (in German)

He Q, Zhi H, Tang S, Xing L, Wang S, Wang H, Zhang A, Li Y, Gao M, Zhang H, Chen G, Dai S, Li J, Yang J, Liu H, Zhang W, Jia Y, Li S, Liu J, Qiao Z, et al. 2020. QTL mapping for foxtail millet plant height in multi-environment using an ultra-high density bin map. Theoretical and Applied Genetics134, 557–572.

Huang X H, Wei X H, Sang T, Zhao Q, Feng Q, Zhao Y, Li C Y, Zhu C R, Lu T T. 2010. Genome-wide association studies of 14 agronomic traits in rice landraces. Nature Genetics42, 961–967.

Jia J, Wang H, Cai Z D, Wei R Q, Huang J H, Xia Q J, Xiao X H, Ma Q B, Nian H, Cheng Y B. 2022. Identification and validation of stable and novel quantitative trait loci for pod shattering in soybean [Glycinemax (L.) Merr.]. Journal of Integrative Agriculture21, 3169–3184.

Jiang J, Fan X, Zhang Y, Tang X, Li X, Liu C, Zhang Z. 2020. Construction of a high-density genetic map and mapping of firmness in grapes (Vitis vinifera L.) based on whole-genome resequencing. International Journal of Molecular Sciences21, 797.

Kaur S, Kimber R B, Cogan N O, Materne M, Forster J W, Paull J G. 2014. SNP discovery and high-density genetic mapping in faba bean (Vicia faba L.) permits identification of QTLs for ascochyta blight resistance. Plant Science217, 47–55.

Khazaei H, O’Sullivan D M, Sillanpää M J, Stoddard F L. 2014. Use of synteny to identify candidate genes underlying QTL controlling stomatal traits in faba bean (Vicia faba L.). Theoretical and Applied Genetics127, 2371–2385.

Li H, Ribaut J M, Li Z, Wang J. 2008. Inclusive composite interval mapping (ICIM) for digenic epistasis of quantitative traits in biparental populations. Theoretical and Applied Genetics116, 243–260.

Link W, Dixkens C, Singh M, Schwall M, Melchinger A E. 1995. Genetic diversity in European and Mediterranean faba bean germ-plasm revealed by RAPD markers. Theoretical and Applied Genetics90, 27–32.

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 Journal3, 269–283.

Ocaña-Moral S, Gutiérrez N, Torres A M, Madrid E. 2017. Saturation mapping of regions determining resistance to Ascochyta blight and broomrape in faba bean using transcriptome-based SNP genotyping. Theoretical and Applied Genetics130, 2271–2282.

Ouellette L A, Reid R W, Blanchard S G, Brouwer C R. 2017. LinkageMapView - rendering high-resolution linkage and QTL maps. Bioinformatics34, 306–307.

Patto M, Torres A, Koblizkova A, Macas J, Cubero J I. 1999. Development of a genetic composite map of Vicia faba using F2 populations derived from trisomic plants. Theoretical and Applied Genetics98, 736–743.

Qu P, Shi J, Chen T, Chen K, Shen C, Wang J, Zhao X, Ye G, Xu J, Zhang L. 2020. Construction and integration of genetic linkage maps from three multi-parent advanced generation inter-cross populations in rice. Rice13, 13.

Quint M, Dussle C M, Melchinger A E, Lübberstedt T. 2003. Identification of genetically linked RGAs by BAC screening in maize and implications for gene cloning, mapping and MAS. Theoretical and Applied Genetics106, 1171–1177.

Rastas P. 2017. Lep-MAP3: robust linkage mapping even for low-coverage whole genome sequencing data. Bioinformatics33, 3726–3732.

Ren T, Fan T, Chen S, Li C, Chen Y, Ou X, Jiang Q, Ren Z, Tan F, Luo P, Chen C, Li Z. 2021. Correction to: Utilization of a Wheat55K SNP array-derived high-density genetic map for high-resolution mapping of quantitative trait loci for important kernel-related traits in common wheat. Theoretical and Applied Genetics134, 1601.

Sallam A, Arbaoui M, El-Esawi M, Abshire N, Martsch R. 2016. Identification and verification of QTL associated with frost tolerance using linkage mapping and GWAS in winter faba bean. Frontiers in Plant Science7, 1098.

Satovic Z, Avila C M, Cruz-Izquierdo S, Díaz-Ruíz R, García-Ruíz G M, Palomino C, Gutiérrez N, Vitale S, Ocaña-Moral S, Gutiérrez M V, Cubero J I, Torres A M. 2013. A reference consensus genetic map for molecular markers and economically important traits in faba bean (Vicia faba L.). BMC Genomics14, 932.

Shi M Q, Liao X L, Ye Q, Zhang W, Li Y K, Bhat J A, Kan G Z, Yu D Y. 2022. Linkage and association mapping of wild soybean (Glycine soja) seeds germinating under salt stress. Journal of Integrative Agriculture21, 2833–2847.

Sudheesh S, Kimber R B E, Braich S, Forster J W, Paull J G, Kaur S. 2019. Construction of an integrated genetic linkage map and detection of quantitative trait loci for Ascochyta blight resistance in faba bean (Vicia faba L.). Euphytica215, 42.

Sun X, Gao Y, Lu Y, Zhang X, Luo S, Li X, Liu M, Feng D, Gu A, Chen X, Xuan S, Wang Y, Shen S, Bonnema G, Zhao J. 2021. Genetic analysis of the “head top shape” quality trait of Chinese cabbage and its association with rosette leaf variation. Horticulture Research8, 106.

Terracciano I, Cantarella C, Fasano C, Cardi T, Mennella G, D’Agostino N. 2017. Liquid-phase sequence capture and targeted re-sequencing revealed novel polymorphisms in tomato genes belonging to the MEP carotenoid pathway. Scientific Reports7, 5616.

Tian Y, Yang L, Lu H F, Zhang B, Li Y F, Liu C, Ge T L, Liu Y L, Han J N, Li Y H, Qiu L J. 2022. QTL analysis for plant height and fine mapping of two environmentally stable QTLs with major effects in soybean. Journal of Integrative Agriculture21, 933–946.

Torres A M, Weeden N F, Martín A. 1993. Linkage among isozyme, RFLP and RAPD markers in Vicia fabaTheoretical and Applied Genetics85, 937–945.

Wang C, Liu R, Liu Y, Hou W, Wang X, Miao Y, He Y, Ma Y, Li G, Wang D, Ji Y, Zhang H, Li M, Yan X, Zong X, Yang T. 2021. Development and application of the Faba_bean_130K targeted next-generation sequencing SNP genotyping platform based on transcriptome sequencing. Theoretical and Applied Genetics134, 3195–3207.

Wang H F, Zong X X, Guan J P, Yang T, Sun X L, Ma Y, Redden R. 2012. Genetic diversity and relationship of global faba bean (Vicia faba L.) germplasm revealed by ISSR markers. Theoretical and Applied Genetics124, 789–797.

Wang S, Wong D, Forrest K, Allen A, Chao S, Huang B E, Maccaferri M, Salvi S, Milner S G, Cattivelli L, Mastrangelo A M, Whan A, Stephen S, Barker G, Wieseke R, Plieske J, Lillemo M, Mather D, Appels R, Dolferus R. 2014. Characterization of polyploid wheat genomic diversity using a high-density 90,000 single nucleotide polymorphism array. Plant Biotechnology Journal6, 787–796.

Webb A, Cottage A, Wood T, Khamassi K, Hobbs D, Gostkiewicz K, White M, Khazaei H, Ali M, Street D, Duc G, Stoddard F L, Maalouf F, Ogbonnaya F C, Link W, Thomas J, O’Sullivan D M. 2016. A SNP-based consensus genetic map for synteny-based trait targeting in faba bean (Vicia faba L.). Plant Biotechnology Journal14, 177–185.

Xiong H, Li Y, Guo H, Xie Y, Zhao L, Gu J, Zhao S, Ding Y, Liu L. 2021. Genetic mapping by integration of 55K SNP array and KASP markers reveals candidate genes for important agronomic traits in Hexaploid wheat. Frontiers in Plant Science12, 628478.

Xu C C, Zhang P, Wang Y Y, Luo N, Tian B J, Liu X W, Wang P, Huang S B. 2022. Grain yield and grain moisture associations with leaf, stem and root characteristics in maize. Journal of Integrative Agriculture21, 1941–1951.

Yan M, Byrne D H, Klein P E, Yang J, Dong Q, Anderson N. 2018. Genotyping-by-sequencing application on diploid rose and a resulting high-density SNP-based consensus map. Horticulture Research5, 17.

Yang M J, Wang C R, Hassan M A, Wu Y Y, Xia X C, Shi S B, Xiao Y G, He Z H. 2021. QTL mapping of seedling biomass and root traits under different nitrogen conditions in bread wheat (Triticum aestivum L.). Journal of Integrative Agriculture20, 1180–1192.

Yang T, Jiang J, Zhang H, Liu R, Strelkov S, Hwang S F, Chang K F, Yang F, Miao Y M, He Y H, Zong X X. 2019. Density enhancement of a faba bean genetic linkage map (Vicia faba) based on simple sequence repeats markers. Plant Breeding2, 138.

Yin Y, An W, Zhao J H, Li Y L, Fan Y F, Chen J H, Cao Y L, Zhan X Q. 2022. Constructing the wolfberry (Lycium spp.) genetic linkage map using AFLP and SSR markers. Journal of Integrative Agriculture21, 131–138.

Zhang K, Fan G, Zhang X, Zhao F, Wei W, Du G, Feng X, Wang X, Wang F, Song G, Zou H, Zhang X, Li S, Ni X, Zhang G, Zhao Z. 2017. Identification of QTLs for agronomically important traits in Setaria italica based on SNPs generated from high-throughput sequencing. G3 - Genes Genomes Genetics7, 1587–1594.

Zhou G, Jian J, Wang P, Li C, Tao Y, Li X, Renshaw D, Clements J, Sweetingham M, Yang H. 2018. Construction of an ultra-high density consensus genetic map, and enhancement of the physical map from genome sequencing in Lupinus angustifoliusTheoretical and Applied Genetics131, 209–223.

Zong X X, Bao S Y, Guan J P, Wang X O, Wang Z G. 2006. Descriptors and Data Standard for Faba Bean (Vicia faba L.). China Agriculture Press, Beijing. pp. 9–23. (in Chinese)

[1] LIU Dan, ZHAO De-hui, ZENG Jian-qi, Rabiu Sani SHAWAI, TONG Jing-yang, LI Ming, LI Fa-ji, ZHOU Shuo, HU Wen-li, XIA Xian-chun, TIAN Yu-bing, ZHU Qian, WANG Chun-ping, WANG De-sen, HE Zhong-hu, LIU Jin-dong, ZHANG Yong. Identification of genetic loci for grain yield‑related traits in the wheat population Zhongmai 578/Jimai 22[J]. >Journal of Integrative Agriculture, 2023, 22(7): 1985-1999.
[2] XIAO Jing-xiu, ZHU Ying-an, BAI Wen-lian, LIU Zhen-yang, TANG Li, ZHENG Yi. Yield performance and optimal nitrogen and phosphorus application rates in wheat and faba bean intercropping[J]. >Journal of Integrative Agriculture, 2021, 20(11): 3012-3025.
[3] GONG Ya-ming, XU Sheng-chun, MAO Wei-hua, LI Ze-yun, HU Qi-zan, ZHANG Gu-wen and DING Ju. Genetic Diversity Analysis of Faba Bean (Vicia faba L.) Based on EST-SSR Markers[J]. >Journal of Integrative Agriculture, 2011, 10(6): 838-844.
No Suggested Reading articles found!