Identification and characterization of long-InDels through whole genome resequencing to facilitate fine-mapping of a QTL for plant height in soybean (Glycine max L. Merr.)

doi:10.1016/S2095-3119(21)63675-4

Journal of Integrative Agriculture

2022, Vol. 21

Issue (7): 1903-1912 DOI: 10.1016/S2095-3119(21)63675-4

Special Issue: 油料作物合辑Oil Crops

Crop Science

Advanced Online Publication | Current Issue | Archive | Adv Search

Identification and characterization of long-InDels through whole genome resequencing to facilitate fine-mapping of a QTL for plant height in soybean (Glycine max L. Merr.)

LIU Chen^{1, 2*}, TIAN Yu^2*, LIU Zhang-xiong², GU Yong-zhe², ZHANG Bo³, LI Ying-hui², NA Jie¹, QIU Li-juan²

¹School of Life Sciences, Liaoning Normal University, Dalian 116081, P.R.China
² National Key Facility for Gene Resources and Genetic Improvement/Key Laboratory of Crop Germplasm Utilization, Ministry of Agriculture and Rural Affairs/Institute of Crop Sciences, Chinese Academy of Agricultural Science, Beijing 100081, P.R.China
³ School of Plant and Environmental Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24060, USA

Abstract
References

Download: PDF in ScienceDirect
Export: BibTeX | EndNote (RIS)

摘要

本研究在前期已发掘短片段InDels和SNPs基础上，基于全基因组重测序分析在一个重组自交系群体的两个亲本中品03-5373（ZP）和中黄13（ZH）之间检测到不均匀分布在大豆20条染色体上的13573个长片段InDels，其中，Chr11上最少，有321个，Chr18上最多，有1246个。长片段InDels在染色体两臂的平均密度显著高于着丝粒区，与大豆基因组注释基因的分布模式一致。位于基因区的长片段InDels有2704个，占总数目的19.9%，其中319个为可导致蛋白质序列截短或延长的大效应InDels。重点对前期鉴定的株高相关QTL（qPH16）进行分析，共鉴定到35个长片段InDels，并将其开发成InDel标记，其中26个InDel标记（74.3%）在ZP和ZH之间表现出明显的多态性。利用开发的标记结合已有的4个SNPs标记对由ZP和ZH衍生的242个重组自交系进行基因型鉴定和QTL定位，将qPH16的定位区间从原来的960 kb缩小到477.55 kb，包含65个注释基因。在SNPs和短片段InDels开发基础上，进一步开发长片段InDels，可为大豆重要农艺性状的遗传分析和分子辅助选择育种提供更加全面的遗传变异信息。

Abstract With the development of sequencing technology, insertions-deletions (InDels) have been increasingly reported to be involved in the genetic deter mination of agronomical traits. However, most studies have focused on the identification and application of short-InDels (1–15 bp) for genetic analysis. The objective of this study was to deeply deploy long-InDels (>15 bp) for the genetic analysis of important agronomic traits in soybean. A total of 13 573 polymorphic long-InDels were identified between parents Zhongpin 03-5373 (ZP) and Zhonghuang 13 (ZH), which were unevenly distributed on 20 chromosomes of soybean, varying from 321 in Chr11 to 1 246 in Chr18. Consistent with the distribution pattern of annotated genes, the average density of long-InDels in arm regions was significantly higher than that in pericentromeric regions at the P=0.01 level. A total of 2 704 (19.9% of total) long-InDels were located in genic regions, including 319 large-effect long-InDels, which resulted in truncated or elongated protein sequences. A previously identified QTL (qPH16) underlying plant height was further analyzed, and it was found that 26 out of 35 (74.3%) long-InDel markers located in the qPH16 region showed clear polymorphisms between parents ZP and ZH. Seven markers, including three long-InDels and four previously reported SNP markers, were used to genotype 242 recombinant inbred lines derived from ZP×ZH. As a result, the qPH16 locus was narrowed from a 960-kb region to a 477.55-kb region, containing 65 annotated genes. Therefore, these long-InDels are a complementary genetic resource of SNPs and short-InDels for plant height and can facilitate genetic studies and molecular assisted selection breeding in soybean.

Keywords: soybean plant height whole genome re-sequencing long-InDels QTL

Received: 25 November 2020 Accepted: 03 March 2021

Fund: This research was supported by the National Key R&D Program of China (2016YFD0100201 and 2020YFE0202300) and the Agricultural Science and Technology Innovation Program (ASTIP) of the Chinese Academy of Agricultural Sciences.

About author: LIU Chen, E-mail: 1518753786@qq.com; TIAN Yu, E-mail: 82101181082@caas.cn; Correspondence QIU Li-juan, E-mail: qiulijuan@caas.cn; NA Jie, Tel: +86-411-85827090, E-mail: jiena@lnnu.edu.cn; LI Ying-hui, Tel: +86-10-82105843, E-mail: liyinghui@caas.cn * These authors contributed equally to this study.

	Service
	E-mail this article
	Add to citation manager
	E-mail Alert
	RSS

	Articles by authors
	LIU Chen
	TIAN Yu
	LIU Zhang-xiong
	GU Yong-zhe
	ZHANG Bo
	LI Ying-hui
	NA Jie
	QIU Li-juan

Cite this article:

LIU Chen, TIAN Yu, LIU Zhang-xiong, GU Yong-zhe, ZHANG Bo, LI Ying-hui, NA Jie, QIU Li-juan. 2022. Identification and characterization of long-InDels through whole genome resequencing to facilitate fine-mapping of a QTL for plant height in soybean (Glycine max L. Merr.). Journal of Integrative Agriculture, 21(7): 1903-1912.

Arahana V S, Graef G L, Specht J E, Steadman J R, Eskridge K M. 2001. Identification of QTLs for resistance to Sclerotinia sclerotiorum in soybean. Crop Science, 41, 180–188.
Britten R J, Rowen L, Williams J, Cameron R A. 2003. Majority of divergence between closely related DNA samples is due to InDels. Proceedings of the National Academy of Sciences of the United States of America, 100, 4661–4665.
Concibido V C, Lange D A, Denny R L, Orf J H, Young N D. 1997. Genome mapping of soybean cyst nematode resistance genes in ‘Peking’, PI 90763, and PI 88788 using DNA markers. Crop Science, 37, 258–264.
Dangl J L, Jones J D G. 2001. Plant pathogens and integrated defence responses to infection. Nature, 411, 826–833.
Doyle J J, Doyle J L. 1990. Isolation of plant DNA from fresh tissue. Focus, 12, 13–15.
Fang C, Ma Y M, Wu S W, Liu Z, Wang Z, Yang R, Hu G H, Zhou Z K, Yu H, Zhang M, Pan Y, Zhou G A, Ren H X, Du W G, Yan H R, Wang Y P, Han D Z, Shen Y T, Liu S L, Liu T F, et al. 2017. Genome-wide association studies dissect the genetic networks underlying agronomical traits in soybean. Genome Biology, 18, 161.
Ferreira M F D S, Cervigni G D L, Ferreira A, Schuster I, Moreira M A, Santana F A, Pereira W D, Barros E G D, Moreira M A. 2011. QTLs for resistance to soybean cyst nematode, races 3, 9, and 14 in cultivar Hartwig. Pesquisa Agropecuária Brasilra, 46, 420–428.
Guo X M, Wang D C, Gordon S G, Helliwell E, Smith T, Berry S A, St Martin S K, Dorrance A E. 2008. Genetic mapping of QTLs underlying partial resistance to Sclerotinia sclerotiorum in soybean PI 391589A and PI 391589B. Crop Science, 48, 1129–1139.
Guzman P S, Diers B W, Neece D J, St Martin S K, LeRoy A R, Grau C R, Hughes T J, Nelson R L. 2007. QTL associated with yield in three backcross-derived populations of soybean. Crop Science, 47, 111–122.
Hey D, Grimm B. 2018. ONE-HELIX PROTEIN2 (OHP2) is required for the stability of OHP1 and assembly factor HCF244 and is functionally linked to PSII biogenesis. Plant Physiology, 177, 1453–1472.
Hey D, Grimm B. 2020. ONE-HELIX PROTEIN1 and 2 form heterodimers to bind chlorophyll in photosystem II biogenesis. Plant Physiology, 183, 179–193.
Lam H M, Xu X, Liu X, Chen W B, Yang G H, Wong F L, Li M W, He W M, Qin N, Wang B, Li J, Jian M, Wang J, Shao G H, Wang J, Sun S S, Zhang G Y. 2010. Resequencing of 31 wild and cultivated soybean genomes identifies patterns of genetic diversity and selection. Nature Genetics, 42, 1053–1059.
Ji F Y, Wei W, Liu Y, Wang G P, Zhang Q, Xing Y, Zhang S H, Liu Z H, Cao Q Q, Qin L. 2018. Construction of a SNP-based high-density genetic map using Genotyping by Sequencing (GBS) and QTL analysis of nut traits in Chinese chestnut (Castanea mollissima Blume). Frontiers in Plant Science, 9, 816.
Jiao Y Q, Vuong T D, Liu Y, Meinhardt C, Liu Y, Joshi T, Cregan P B, Xu D, Shannon J G, Nguyen H T. 2015. Identification and evaluation of quantitative trait loci underlying resistance to multiple HG types of soybean cyst nematode in soybean PI 437655. Theoretical and Applied Genetics, 128, 15–23.
Lark K G, Chase K, Adler F, Mansur L M, Orf J H. 1995. Interactions between quantitative trait loci in soybean in which trait variation at one locus is conditional upon a specific allele at another. Proceedings of the National Academy of Sciences of the United States of America, 92, 4656–4660.
Lee S, Jun T H, Michel A P, Mian M A R. 2015. SNP markers linked to QTL conditioning plant height, lodging, and maturity in soybean. Euphytica, 203, 521–532.
Lee S, Mian M A R, McHale L K, Wang H, Wijeratne A J, Sneller C H, Dorrance A E. 2013. Novel quantitative trait loci for partial resistance to Phytophthora sojae in soybean PI 398841. Theoretical and Applied Genetics, 126, 1121–1132.
Lee S H, Bailey M A, Mian M A R, Carter T E, Ashley D A, Hussey R S, Parrott W A, Boerma H R. 1996. Molecular markers associated with soybean plant height, lodging, and maturity across locations. Crop Science, 36, 728–735.
Li H, Durbin R. 2009. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics, 25, 1754–1760.
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.
Li X P, Han Y P, Teng W L, Zhang S Z, Yu K F, Poysa V, Anderson T, Ding J J, Li W B. 2010. Pyramided QTL underlying tolerance to Phytophthora root rot in mega-environments from soybean cultivars ‘Conrad’ and ‘Hefeng 25’. Theoretical and Applied Genetics, 121, 651–658.
Li Y H, Liu B, Reif J C, Liu Y L, Li H H, Chang R Z, Qiu L J. 2014. Development of insertion and deletion markers based on biparental resequencing for fine mapping seed weight in soybean. Plant Genome, 7, 1–8.
Li Y H, Shi X H, Li H H, Reif J C, Wang J J, Liu Z X, He S, Yu B S, Qiu L J. 2016. Dissecting the genetic basis of resistance to soybean cyst nematode combining linkage and association mapping. Plant Genome, 9, 1–11.
Li Y H, Zhao S C, Ma J X, Li D, Yan L, Li J, Qi X T, Guo X S, Zhang L, He W M, Chang R Z, Liang Q S, Guo Y, Ye C, Wang X B, Tao Y, Guan R X, Wang J Y, Liu Y L, Jin L G, et al. 2013. Molecular footprints of domestication and improvement in soybean revealed by whole genome re-sequencing. BMC Genomics, 14, 579.
Liu N X, Li M, Hu X B, Ma Q B, Mu Y H, Tan Z Y, Xia Q J, Zhang G Y, Nian H. 2017. Construction of high-density genetic map and QTL mapping of yield-related and two quality traits in soybean RILs population by RAD-sequencing. BMC Genomics, 18, 466.
Liu Y C, Du H L, Li P C, Shen Y T, Peng H, Liu S L, Zhou G A, Zhang H K, Liu Z, Shi M, Huang X H, Li Y, Zhang M, Wang Z, Zhu B, Han B, Liang C Z, Tian Z X. 2020. Pan-genome of wild and cultivated soybeans. Cell, 182, 162–176.
Liu Y L, Li Y H, Reif J C, Mette M F, Liu Z X, Liu B, Zhang S S, Yan L, Chang R Z, Qiu L J. 2013. Identification of quantitative trait loci underlying plant height and seed weight in soybean. Plant Genome, 6, 1–11.
Mansur L M, Orf J, Lark K G. 1993. Determining the linkage of quantitative trait loci to RFLP markers using extreme phenotypes of recombinant inbreds of soybean (Glycine max L. Merr.). Theoretical and Applied Genetics, 86, 914–918.
Mansur L M, Orf J H, Chase K, Jarvik T, Cregan P B, Lark K G. 1996. Genetic mapping of agronomic traits using recombinant inbred lines of soybean. Crop Science, 36, 1327–1336.
Patil G, Chaudhary J, Vuong T D, Jenkins B, Qiu D, Kadam S, Shannon G J, Nguyen H T. 2017. Development of SNP genotyping assays for seed composition traits in soybean. International Journal of Plant Genomics, 2017, 1–12.
Qiu B X, Arelli P R, Sleper D A. 1999. RFLP markers associated with soybean cyst nematode resistance and seed composition in a ‘Peking’×‘Essex’ population. Theoretical and Applied Genetics, 98, 356–364.
Shen Y T, Liu J, Geng H Y, Zhang J X, Liu Y C, Zhang H K, Xing S L, Du J C, Ma S S, Tian Z X. 2018. De novo assembly of a Chinese soybean genome. Science China (Life Sciences), 61, 871–884.
Shi Z, Liu S M, Noe J, Arelli P, Meksem K, Li Z L. 2015. SNP identification and marker assay development for high-throughput selection of soybean cyst nematode resistance. BMC Genomics, 16, 314.
Song Q J, Jenkins J, Jia G F, Hyten D L, Pantalone V, Jackson S A, Schmutz J, Cregan P B. 2016. Construction of high resolution genetic linkage maps to improve the soybean genome sequence assembly Glyma1.01. BMC Genomics, 17, 33.
Song X F, Wei H C, Cheng W, Yang S X, Zhao Y X, Li X, Luo D, Zhang H, Feng X Z. 2015. Development of InDel markers for genetic mapping based on whole genome resequencing in soybean. G3 - Genes Genomes Genetics, 5, 2793–2799.
Springer N M, Ying K, Fu Y, Ji T M, Yeh C T, Jia Y, Wu W, Richmond T, Kitzman J, Rosenbaum H, Iniguez A L, Barbazuk W B, Jeddeloh J A, Nettleton D, Schnable P S. 2009. Maize inbreds exhibit high levels of copy number variation (CNV) and presence/absence variation (PAV) in genome content. PLoS Genetics, 5, e1000734.
Tucker D M, Maroof M A S, Mideros S, Skoneczka J A, Nabati D A, Buss G R, Hoeschele I, Tyler B M, St Martin S K, Dorrance A E. 2010. Mapping quantitative trait loci for partial resistance to Phytophthora sojae in a soybean interspecific cross. Crop Science, 50, 628–635.
Wang D, Graef G L, Procopiuk A M, Diers B W. 2004. Identification of putative QTL that underlie yield in interspecific soybean backcross populations. Theoretical and Applied Genetics, 108, 458–467.
Wang K, Li M Y, Hakonarson H. 2010. ANNOVAR: Functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Research, 38, e164.
Xia N, Yan W B, Wang X Q. Shao Y P, Yang M M, Wang Z K, Zhan Y H, Teng W L, Han Y P, Shi Y G. 2019. Genetic dissection of hexanol content in soybean seed through genome-wide association analysis. Journal of Integrative Agriculture, 18, 1222–1229.
Yan L, Li Y H, Yang C Y, Ren S X, Chang R Z, Zhang M C, Qiu L J. 2015. Identification and validation of an over-dominant QTL controlling soybean seed weight using populations derived from Glycine max×Glycine soja. Plant Breeding, 133, 632–637.
Yang L, Tian Y, Liu Y L, Reif J C, Li Y H, Qiu L J. 2021. QTL mapping of qSCN3-1 for resistance to soybean cyst nematode in soybean line Zhongpin 03-5373. The Crop Journal, 9, 351–359.
Yu C, Wan H H, Peter M B, Cheng B X, Luo L, Pan H T, Zhang Q X. 2021. High density genetic map and quantitative trait loci (QTLs) associated with petal number and flower diameter identified in tetraploid rose. Journal of Integrative Agriculture, 20, 1287–1301.
Yue P, Sleper D A, Arelli P R. 2001. Mapping resistance to multiple races of Heterodera glycines in soybean PI 89772. Crop Science, 41, 1589–1595.
Zhang G R, Gu C H, Wang D C. 2009. Molecular mapping of soybean aphid resistance genes in PI 567541B. Theoretical and Applied Genetics, 118, 473–482.
Zhang J P, Song Q J, Cregan P B, Jiang G L. 2016. Genome-wide association study, genomic prediction and marker-assisted selection for seed weight in soybean (Glycine max). Theoretical and Applied Genetics, 129, 117–130.
Zhou Z K, Jiang Y, Wang Z, Gou Z H, Lyu J, Li W Y, Yu Y J, Shu L P, Zhao Y J, Ma Y M, Fang C, Shen Y T, Liu T F, Li C C, Li Q, Wu M, Wang M, Wu Y S, Dong Y, Wan W T, et al. 2015. Resequencing 302 wild and cultivated accessions identifies genes related to domestication and improvement in soybean. Nature Biotechnology, 33, 408–414.

[1]	YANG Hong-jun, YE Wen-wu, YU Ze, SHEN Wei-liang, LI Su-zhen, WANG Xing, CHEN Jia-jia, WANG Yuan-chao, ZHENG Xiao-bo. Host niche, genotype, and field location shape the diversity and composition of the soybean microbiome[J]. >Journal of Integrative Agriculture, 2023, 22(8): 2412-2425.
[2]	XU Lei, ZHAO Tong-hua, Xing Xing, XU Guo-qing, XU Biao, ZHAO Ji-qiu. *Model fitting of the seasonal population dynamics of the soybean aphid, Aphis* glycines Matsumura, in the field** [J]. >Journal of Integrative Agriculture, 2023, 22(6): 1797-1808.
[3]	GAO Hua-wei, YANG Meng-yuan, YAN Long, HU Xian-zhong, HONG Hui-long, ZHANG Xiang, SUN Ru-jian, WANG Hao-rang, WANG Xiao-bo, LIU Li-ke, ZHANG Shu-zhen, QIU Li-juan. Identification of tolerance to high density and lodging in short petiolate germplasm M657 and the effect of density on yield-related phenotypes of soybean[J]. >Journal of Integrative Agriculture, 2023, 22(2): 434-446.
[4]	QU Zheng, LI Yue-han, XU Wei-hui, CHEN Wen-jing, HU Yun-long, WANG Zhi-gang. Different genotypes regulate the microbial community structure in the soybean rhizosphere[J]. >Journal of Integrative Agriculture, 2023, 22(2): 585-597.
[5]	GAO Hua-wei, SUN Ru-jian, YANG Meng-yuan, YAN Long, HU Xian-zhong, FU Guang-hui, HONG Hui-long, GUO Bing-fu, ZHANG Xiang, LIU Li-ke, ZHANG Shu-zhen, QIU Li-juan. Characterization of the petiole length in soybean compact architecture mutant M657 and the breeding of new lines[J]. >Journal of Integrative Agriculture, 2022, 21(9): 2508-2520.
[6]	GAO Ri-xin, HU Ming-jian, ZHAO Hai-ming, LAI Jin-sheng, SONG Wei-bin. Genetic dissection of ear-related traits using immortalized F₂ population in maize [J]. >Journal of Integrative Agriculture, 2022, 21(9): 2492-2507.
[7]	ZHANG Hua, WU Hai-yan, TIAN Rui, KONG You-bin, CHU Jia-hao, XING Xin-zhu, DU Hui, JIN Yuan, LI Xi-huan, ZHANG Cai-ying. Genome-wide association and linkage mapping strategies reveal genetic loci and candidate genes of phosphorus utilization in soybean[J]. >Journal of Integrative Agriculture, 2022, 21(9): 2521-2537.
[8]	ZOU Jia-nan, ZHANG Zhan-guo, KANG Qing-lin, YU Si-yang, WANG Jie-qi, CHEN Lin, LIU Yan-ru, MA Chao, ZHU Rong-sheng, ZHU Yong-xu, DONG Xiao-hui, JIANG Hong-wei, WU Xiao-xia, WANG Nan-nan, HU Zhen-bang, QI Zhao-ming, LIU Chun-yan, CHEN Qing-shan, XIN Da-wei, WANG Jin-hui. Characterization of chromosome segment substitution lines reveals candidate genes associated with the nodule number in soybean[J]. >Journal of Integrative Agriculture, 2022, 21(8): 2197-2210.
[9]	CHAO Kai-xiang, WU Cai-juan, LI Juan, WANG Wen-li, WANG Bao-tong, LI Qiang. Genetic analysis of adult plant, quantitative resistance to stripe rust in wheat landrace Wudubaijian in multi-environment trials[J]. >Journal of Integrative Agriculture, 2022, 21(8): 2305-2318.
[10]	PAN Wen-jing, HAN Xue, HUANG Shi-yu, YU Jing-yao, ZHAO Ying, QU Ke-xin, ZHANG Ze-xin, YIN Zhen-gong, QI Hui-dong, YU Guo-long, ZHANG Yong, XIN Da-wei, ZHU Rong-sheng, LIU Chun-yan, WU Xiao-xia, JIANG Hong-wei, HU Zhen-bang, ZUO Yu-hu, CHEN Qing-shan, QI Zhao-ming. Identification of candidate genes related to soluble sugar contents in soybean seeds using multiple genetic analyses[J]. >Journal of Integrative Agriculture, 2022, 21(7): 1886-1902.
[11]	HUI Fang, XIE Zi-wen, LI Hai-gang, GUO Yan, LI Bao-guo, LIU Yun-ling, MA Yun-tao. Image-based root phenotyping for field-grown crops: An example under maize/soybean intercropping[J]. >Journal of Integrative Agriculture, 2022, 21(6): 1606-1619.
[12]	TIAN Yu, YANG Lei, LU Hong-feng, ZHANG Bo, LI Yan-fei, LIU Chen, GE Tian-li, LIU Yu-lin, HAN Jia-nan, LI Ying-hui, QIU Li-juan. QTL analysis for plant height and fine mapping of two environmentally stable QTLs with major effects in soybean[J]. >Journal of Integrative Agriculture, 2022, 21(4): 933-946.
[13]	JIANG Xue-qian, ZHANG Fan, WANG Zhen, LONG Rui-cai, LI Ming-na, HE Fei, YANG Xi-jiang, YANG Chang-fu, JIANG Xu, YANG Qing-chuan, WANG Quan-zhen, KANG Jun-mei. *Detection of quantitative trait loci (QTL) associated with spring regrowth in alfalfa (Medicago sativa* L.)**[J]. >Journal of Integrative Agriculture, 2022, 21(3): 812-818.
[14]	LIU Sang-lin, CHENG Yan-bo, MA Qi-bin, LI Mu JIANG Ze, XIA Qiu-ju, NIAN Hai. *Fine mapping and genetic analysis of resistance genes, Rsc18, against soybean mosaic virus*[J]. >Journal of Integrative Agriculture, 2022, 21(3): 644-653.
[15]	LIU Li-feng, GAO Le, ZHANG Li-xin, CAI Yu-peng, SONG Wen-wen, CHEN Li, YUAN Shan, WU Ting-ting, JIANG Bing-jun, SUN Shi, WU Cun-xiang, HOU Wen-sheng, HAN Tian-fu. Co-silencing E1 and its homologs in an extremely late-maturing soybean cultivar confers super-early maturity and adaptation to high-latitude short-season regions[J]. >Journal of Integrative Agriculture, 2022, 21(2): 326-335.

No Suggested Reading articles found!

Viewed

Full text

Abstract

Cited

Shared

Discussed

Cite this article:

About JIA

Editorial board

For authors