Identification of candidate gene controlling shade-tolerant by BSA-Seq in soybean

doi:10.19802/j.issn.1007-9084.2020358

Abstract

Abstract:

Intercropping patterns of soybean is an important model in southern China, the shading stress of high stalk crops is an important factor that affects the yield and quality of intercropped soybean. Therefore, it is particularly important to analyze the shade tolerance of soybean. In this study, a recombinant inbred lines （RILs） established from the shade-tolerant （Aijiaozao） and shade-sensitive （Chippewa）, 30 shade-tolerant and shade-sensitive accessions were selected to construct two DNA hybrid pools, respectively. Progeny hybrid and parent pools were covered for an average depth of 60× and 30×. By calculating the SNP-index of two progeny pools, the differences of SNP-index between shade-tolerant and shade-sensitive chromosomal segments were compared. And the candidate genes of shade tolerance were predicted based on their functional annotations. The results showed that 11 963 077 single nucleotide polymorphisms （SNPs） were obtained from four samples. There were 408 genes were found that they were mainly located on chromosome1 （51 942-505 708 bp）, chr. 4 （50 972 768-51 854 631 bp）, chr. 9 （48 778 767-50 178 743 bp） and chr. 18 （40 858 027-43 909 456 bp）. According to gene annotation and functional analysis, five candidate genes might be related to shade tolerance of soybean, including 1-aminocyclopropane-1-carboxylate oxidase 5-like, auxin-induced protein 5NG4-like, phytochrome-associated serine/threonine protein phosphatase-like, MYBJ6 and MYB128 were identified. They might play an important role in the process of soybean shade tolerance. The results will lay an important foundation for the molecular mechanism of soybean shade tolerance, and laid solid theoretical foundation for map-based cloning of shade-tolerant genes in soybean.

Key words: soybean, shade tolerance, BSA-Seq, candidate gene

CLC Number:

S565.1

Wei-ming ZENG, Yan-zhu SU, Zhen-guang LAI, Shou-zhen YANG, Huai-zhu CHEN, Yu-rong TAN, Zu-dong SUN, Jun-yi GAI. Identification of candidate gene controlling shade-tolerant by BSA-Seq in soybean[J]. CHINESE JOURNAL OF OIL CROP SCIENCES, 2021, 43(6): 1006-1015.

Figures/Tables 5

Table 1

Table 2

Table 3

Fig. 1

Table 4

Gene information in the candidate regions

编号 NO.	基因编号 Gene ID	基因注释 Gene description	染色体 Chromosome	功能预测 Functional analysis
1	LOC778053	MYB转录因子MYB128 MYB transcription factor MYB128	Chr1	RNA生物合成-转录调控 RNA biosynthesis. transcriptional regulation
2	LOC778160	MYB转录因子MYBJ6 MYB transcription factor MYBJ6	Chr1	RNA生物合成-转录调控 RNA biosynthesis. transcriptional regulation
3	LOC100819082	MYB/HD转录因子 MYB/HD-like transcription factor	Chr18	RNA生物合成-转录调控 RNA biosynthesis. transcriptional regulation
4	LOC100805768	含NAC结构域的蛋白质 NAC domain-containing protein	Chr4	RNA生物合成-转录调控 RNA biosynthesis. transcriptional regulation
5	LOC100805895	WRKY转录因子WRKY70 Probable WRKY transcription factor 70-like	Chr9	RNA生物合成-转录调控 RNA biosynthesis. transcriptional regulation
6	LOC547722	DIM 1蛋白 DIM 1-like protein	Chr9	RNA加工-前体mRNA剪接 RNA processing. pre-mRNA splicing
7	LOC100785211	含G补丁结构域蛋白质 G-patch domain-containing protein	Chr9	RNA加工-前体mRNA剪接 RNA processing. pre-mRNA splicing
8	LOC100306084	蛋白酶体?亚基C1 Putative proteasome beta subunit C1	Chr4	蛋白质内稳态-泛素蛋白酶体系统 Protein homeostasis. ubiquitin-proteasome system
9	LOC100306051	延长因子P Elongation factor P	Chr9	蛋白质生物合成-细胞组织 Protein biosynthesis. organelle machinery
10	LOC100805081	光敏色素相关丝氨酸/苏氨酸蛋白磷酸酶 Phytochrome-associated serine/threonine protein phosphatase-like	Chr9	蛋白质修饰-磷酸化 Protein modification. Phosphorylation
11	LOC100819620	丝氨酸/苏氨酸蛋白激酶NAK Probable serine/threonine-protein kinase NAK-like	Chr18	蛋白质修饰-磷酸化 Protein modification. Phosphorylation
12	LOC100804819	S6激酶1 S6 Kinase 1	Chr9	蛋白质修饰-磷酸化 Protein modification. Phosphorylation
13	LOC100272201	不含赖氨酸激酶10 With no lysine kinase 10	Chr9	蛋白质修饰-磷酸化 Protein modification. Phosphorylation
14	LOC100794523	inositol oxygenase 2-like 肌醇加氧酶2	Chr1	碳水化合物代谢-核苷酸糖生物合成 Carbohydrate metabolism. nucleotide sugar biosynthesis
15	LOC778158	UDP糖焦磷酸化酶 UDP-sugar pyrophosphorylase	Chr4	碳水化合物代谢-核苷酸糖生物合成 Carbohydrate metabolism. nucleotide sugar biosynthesis
16	LOC100776301	GDP-L聚焦合酶2 Putative GDP-L-fucose synthase 2-lik	Chr9	碳水化合物代谢-核苷酸糖生物合成 Carbohydrate metabolism. nucleotide sugar biosynthesis
17	LOC100527431	磷脂酶A2 Phospholipase A2	Chr1	脂类代谢-脂类降解 Lipid metabolism. lipid degradation
18	LOC100797904	磷脂酶A2同源物3 Phospholipase A2 homolog 3-like	Chr1	脂类代谢-脂类降解 Lipid metabolism. lipid degradation
19	LOC100775781	氧甾醇结合蛋白相关蛋白3B Oxysterol-binding protein-related protein 3B-like	Chr18	脂类代谢-脂类降解 Lipid metabolism. lipid trafficking
20	LOC100811114	生长素诱导蛋白5NG4 Auxin-induced protein 5NG4-like	Chr4	溶质运移-载体转运 Solute transport. carrier-mediated transport
21	LOC100170705	二硫化物异构酶蛋白 Protein disulfide isomerase-like protein	Chr4	酶分类- EC_5异构酶 Enzyme classification. EC_5 isomerases
22	LOC100818520	细胞色素P450 71D11 Cytochrome P450 71D11-like	Chr9	酶分类- EC_1氧化还原酶 Enzyme classification. EC_1 oxidoreductases
23	LOC100779492	异甘草素2-O-甲基转移酶 Isoliquiritigenin 2'-O-methyltransferase-like	Chr9	酶分类- EC_2转移酶 Enzyme classification. EC_2 transferases
24	LOC100796909	1-氨基环丙烷1-羧酸氧化酶5（ACC 氧化酶5） 1-aminocyclopropane-1-carboxylate oxidase 5-like	Chr4	植物激素作用-乙烯 Phytohormone action. Ethylene
25	LOC100499644	FERONIA受体激酶 FERONIA receptor-like kinase	Chr9	植物激素作用-信号肽 Phytohormone action. signalling peptides
26	LOC548095	氨基酮戊酸盐，δ-脱水酶 Aminolevulinate， delta-， dehydratase	Chr4	辅酶代谢-四吡咯生物合成 Coenzyme metabolism. tetrapyrrol biosynthesis
27	LOC100500425	泛酸?-丙氨酸连接酶蛋白 Pantoate--beta-alanine ligase-like protein	Chr18	辅酶代谢-辅酶A生物合成 Coenzyme metabolism. coenzyme A biosynthesis
28	LOC100795951	蛋白质精氨酸N -甲基转移酶1 Probable protein arginine N-methyltransferase 1-like	Chr1	染色质组织-组蛋白修饰 Chromatin organisation. histone modifications
29	LOC547781	有丝分裂细胞周期蛋白a2类型 Mitotic cyclin a2-type	Chr4	细胞周期组织-细胞周期调控 Cell cycle organisation. cell cycle control
30	LOC 100500292	硫氧还蛋白 Thioredoxin-like protein	Chr4	氧化还原内稳态-叶绿体氧化还原内稳态 Redox homeostasis. chloroplast redox homeostasis
31	LOC 100804314	囊泡相关膜蛋白726 Putative vesicle-associated membrane protein 726-like	Chr18	囊泡运输- SNARE目标膜识别和融合复合物 Vesicle trafficking. SNARE target membrane recognition and fusion complexes
32	LOC 100499919	含ATPase激活剂结构域的蛋白质 ATPase activator domain-containing protein	Chr1	-
33	LOC 100813615	含AP2结构域的转录因子6 AP2 domain-containing transcription factor 6	Chr4	-
34	LOC 100527117	钙结合蛋白 Putative calcium-binding protein	Chr4	-
35	LOC 100526881	环/ U-盒超家族蛋白 RING/U-box superfamily protein	Chr4	-
36	LOC 100806828	含TLC结构域蛋白质2 TLC domain-containing protein 2-like	Chr4	-
37	LOC 100808386	四肽重复蛋白1 Tetratricopeptide repeat protein 1-like	Chr18	-
38	LOC 100306706	AAI_LTSS超家族蛋白 AAI_LTSS superfamily protein	Chr9	-
39	LOC 100815671	阳离子过氧化物酶1 Cationic peroxidase 1-like	Chr9	-
40	LOC 100798447	受体蛋白EIX2 Receptor-like protein EIX2-like	Chr9	-
41	LOC 100527576	含Sel1重复序列蛋白 Sel1 repeat-containing protein	Chr9	-
42	LOC 100819056	可溶性NSF附着蛋白SNAP09 Soluble NSF attachment protein SNAP09	Chr9	-

Table 4

References 51

1	任梦露，刘卫国，刘婷，等. 荫蔽胁迫下大豆茎秆形态建成的转录组分析［J］. 作物学报， 2016， 42（9）： 1319-1331. DOI：10.3724/SP.J.1006.2016.01319. doi: 10.3724/SP.J.1006.2016.01319
2	王竹，杨文钰，伍晓燕，等. 玉米株型和幅宽对套作大豆初花期形态建成及产量的影响［J］. 应用生态学报， 2008（2）： 323-329.
3	王一，杨文钰，张霞，等. 不同生育时期遮阴对大豆形态性状和产量的影响［J］. 作物学报， 2013， 39（10）： 1871-1879. DOI：10.3724/SP.J.1006.2013.01871. doi: 10.3724/SP.J.1006.2013.01871
4	Zhang J， Donald L S， Liu W G， et al. Effects of shade and drought stress on soybean hormones and yield of main-stem and branch［J］. Afr J Biotechnol， 2011， 10（65）： 14392-14398. DOI：10.5897/ajb11.2143. doi: 10.5897/ajb11.2143
5	刘卫国，邹俊林，袁晋，等. 套作大豆农艺性状研究［J］. 中国油料作物学报， 2014， 36（2）： 219-223. DOI：10.7505/j.issn.1007-9084.2014.02.012. doi: 10.7505/j.issn.1007-9084.2014.02.012
6	陈小林，杨文钰，陈忠群，等. 不同施氮水平下净、套作大豆茎秆特征比较研究［J］. 大豆科学， 2011， 30（1）： 101-104.
7	任梦露，刘卫国，刘小明，等. 荫蔽信号对大豆幼苗生长和光合特性的影响［J］. 中国生态农业学报， 2016， 24（4）： 499-505. DOI：10.13930/j.cnki.cjea.151092. doi: 10.13930/j.cnki.cjea.151092
8	罗玲，于晓波，万燕，等. 套作大豆苗期倒伏与茎秆内源赤霉素代谢的关系［J］. 中国农业科学， 2015， 48（13）： 2528-2537. DOI：10.3864/j.issn.0578-1752.2015.13.005. doi: 10.3864/j.issn.0578-1752.2015.13.005
9	李春红，姚兴东，鞠宝韬，等. 不同基因型大豆耐荫性分析及其鉴定指标的筛选［J］. 中国农业科学， 2014， 47（15）： 2927-2939. DOI：10.3864/j.issn.0578-1752.2014.15.003. doi: 10.3864/j.issn.0578-1752.2014.15.003
10	孙祖东，张志鹏，蔡昭艳，等. 大豆耐荫性评价体系的建立与中国南方大豆资源耐荫性变异［J］. 中国农业科学， 2017， 50（5）： 792-801. DOI：10.3864/j.issn.0578-1752.2017.05.002. doi: 10.3864/j.issn.0578-1752.2017.05.002
11	武晓玲，梁海媛，杨峰，等. 大豆苗期耐荫性综合评价及其鉴定指标的筛选［J］. 中国农业科学， 2015， 48（13）： 2497-2507. DOI：10.3864/j.issn.0578-1752.2015.13.002. doi: 10.3864/j.issn.0578-1752.2015.13.002
12	邹俊林，刘卫国，袁晋，等. 套作大豆苗期茎秆木质素合成与抗倒性的关系［J］. 作物学报， 2015， 41（7）： 1098-1104. DOI：10.3724/SP.J.1006.2015.01098. doi: 10.3724/SP.J.1006.2015.01098
13	邓榆川，刘卫国，袁小琴，等. 套作大豆苗期茎秆纤维素合成代谢与抗倒性的关系［J］. 应用生态学报， 2016， 27（2）： 469-476. DOI：10.13287/j.1001-9332.201602.024. doi: 10.13287/j.1001-9332.201602.024
14	罗晓峰，孟永杰，刘卫国，等. 大豆响应荫蔽胁迫的形态及生理机制研究［J］. 分子植物育种， 2018， 16（3）： 979-988. DOI：10.13271/j.mpb.016.000979. doi: 10.13271/j.mpb.016.000979
15	Takagi H， Tamiru M， Akira A， et al. MutMap accelerates breeding of a salt-tolerant rice cultivar［J］. Nat biotechnol， 2015， 33： 445–449.
16	Xia C， Chen L L， Rong T Z， et al. Identification of a new maize inflorescence meristem mutant and association analysis using SLAF-seq method［J］. Euphytica， 2015， 202（1）： 35-44. DOI：10.1007/s10681-014-1202-5. doi: 10.1007/s10681-014-1202-5
17	Han Y， Lv P， Hou S， et al. Combining next generation sequencing with bulked segregant analysis to fine map a stem moisture locus in Sorghum （Sorghum bicolor L. moench）［J］. PLoS One， 2015， 10（5）： e0127065. DOI：10.1371/journal.pone.0127065. doi: 10.1371/journal.pone.0127065
18	Song Q， Jenkins J， Jia G， et al. Construction of high resolution genetic linkage maps to improve the soybean genome sequence assembly Glyma1.01［J］. BMC Genomics， 2016， 17： 33. DOI：10.1186/s12864-015-2344-0. doi: 10.1186/s12864-015-2344-0
19	Doyle J J， Doyle J L. Isolation of plant DNA from fresh tissue［J］. Focus， 1990， 12： 13–15.
20	Li H， Durbin R. Fast and accurate short-read alignment with Burrows-Wheeler transform［J］. Bioinformatics， 2009， 25（14）： 1754-1760. DOI：10.1093/bioinformatics/btp324. doi: 10.1093/bioinformatics/btp324
21	Li H， Durbin R. Fast and accurate long-read alignment with Burrows-Wheeler transform［J］. Bioinformatics， 2010， 26（5）： 589-595. DOI：10.1093/bioinformatics/btp698. doi: 10.1093/bioinformatics/btp698
22	McKenna A， Hanna M， Banks E， et al. The Genome Analysis Toolkit： a MapReduce framework for analyzing next-generation DNA sequencing data［J］. Genome Res， 2010， 20（9）： 1297-1303. DOI：10.1101/gr.107524.110. doi: 10.1101/gr.107524.110
23	Boeva V， Popova T， Bleakley K， et al. Control-FREEC： a tool for assessing copy number and allelic content using next-generation sequencing data［J］. Bioinformatics， 2012， 28（3）： 423-425. DOI：10.1093/bioinformatics/btr670. doi: 10.1093/bioinformatics/btr670
24	Wang K， Li M， Hakonarson H. ANNOVAR： functional annotation of genetic variants from high-throughput sequencing data［J］. Nucleic Acids Res， 2010， 38（16）： e164. DOI：10.1093/nar/gkq603. doi: 10.1093/nar/gkq603
25	Magwene P M， Willis J H， Kelly J K. The statistics of bulk segregant analysis using next generation sequencing［J］. PLoS Comput Biol， 2011， 7（11）： e1002255. DOI：10.1371/journal.pcbi.1002255. doi: 10.1371/journal.pcbi.1002255
26	Yang Z， Huang D， Tang W， et al. Mapping of quantitative trait loci underlying cold tolerance in rice seedlings via high-throughput sequencing of pooled extremes［J］. PLoS One， 2013， 8（7）： e68433. DOI：10.1371/journal.pone.0068433. doi: 10.1371/journal.pone.0068433
27	Li C， Xiang X， Huang Y， et al. Long-read sequencing reveals genomic structural variations that underlie creation of quality protein maize［J］. Nat Commun， 2020， 11（1）： 17. DOI：10.1038/s41467-019-14023-2. doi: 10.1038/s41467-019-14023-2
28	Song J， Li Z， Liu Z， et al. Next-generation sequencing from bulked-segregant analysis accelerates the simultaneous identification of two qualitative genes in soybean［J］. Front Plant Sci， 2017， 8： 919. DOI：10.3389/fpls.2017.00919. doi: 10.3389/fpls.2017.00919
29	Zhong C， Sun S， Li Y， et al. Next-generation sequencing to identify candidate genes and develop diagnostic markers for a novel Phytophthora resistance gene， RpsHC18， in soybean［J］. Theor Appl Genet， 2018， 131（3）： 525-538. DOI：10.1007/s00122-017-3016-z. doi: 10.1007/s00122-017-3016-z
30	张之昊，王俊，刘章雄，等. 基于BSA-Seq技术挖掘大豆中黄622的多小叶基因［J］. 作物学报， 2020， 46： 1839-1849.
31	Liu S L， Wang P， Liu Y T， et al. Identification of candidate gene for resistance to broomrape （Orobanche cumana） in sunflower by BSA-seq［J］. Oil Crop Sci， 2020， 5（2）： 47-51. DOI：10.1016/j.ocsci.2020.05.003. doi: 10.1016/j.ocsci.2020.05.003
32	Zhao C， Zhao G， Geng Z， et al. Physical mapping and candidate gene prediction of fertility restorer gene of cytoplasmic male sterility in cotton［J］. BMC Genomics， 2018， 19（1）： 6. DOI：10.1186/s12864-017-4406-y. doi: 10.1186/s12864-017-4406-y
33	Liang D， Chen M， Qi X， et al. QTL mapping by SLAF-seq and expression analysis of candidate genes for aphid resistance in cucumber［J］. Front Plant Sci， 2016， 7： 1000. DOI：10.3389/fpls.2016.01000. doi: 10.3389/fpls.2016.01000
34	Han Y， Zhao F， Gao S， et al. Fine mapping of a male sterility gene ms-3 in a novel cucumber （Cucumis sativus L.） mutant［J］. Theor Appl Genet， 2018， 131（2）： 449-460. DOI：10.1007/s00122-017-3013-2. doi: 10.1007/s00122-017-3013-2
35	Yin J L， Fang Z W， Sun C， et al. Rapid identification of a stripe rust resistant gene in a space-induced wheat mutant using specific locus amplified fragment （SLAF） sequencing［J］. Sci Rep， 2018， 8（1）： 3086. DOI：10.1038/s41598-018-21489-5. doi: 10.1038/s41598-018-21489-5
36	Nozue K， Tat A V， Kumar Devisetty U， et al. Shade avoidance components and pathways in adult plants revealed by phenotypic profiling［J］. PLoS Genet， 2015， 11（4）： e1004953. DOI：10.1371/journal.pgen.1004953. doi: 10.1371/journal.pgen.1004953
37	Tao Y， Ferrer J L， Ljung K， et al. Rapid synthesis of auxin via a new tryptophan-dependent pathway is required for shade avoidance in plants［J］. Cell， 2008， 133（1）： 164-176. DOI：10.1016/j.cell.2008.01.049. doi: 10.1016/j.cell.2008.01.049
38	Pierik R， Djakovic-Petrovic T， Keuskamp D H， et al. Auxin and ethylene regulate elongation responses to neighbor proximity signals independent of gibberellin and DELLA proteins in Arabidopsis［J］. Plant Physiol， 2009， 149（4）： 1701-1712. DOI：10.1104/pp.108.133496. doi: 10.1104/pp.108.133496
39	Keller M M， Jaillais Y， Pedmale U V， et al. Cryptochrome 1 and phytochrome B control shade-avoidance responses in Arabidopsis via partially independent hormonal cascades［J］. Plant J， 2011， 67（2）： 195-207. DOI：10.1111/j.1365-313x.2011.04598.x. doi: 10.1111/j.1365-313x.2011.04598.x
40	Iglesias M J， Sellaro R， Zurbriggen M D， et al. Multiple links between shade avoidance and auxin networks［J］. J Exp Bot， 2018， 69（2）： 213-228. DOI：10.1093/jxb/erx295. doi: 10.1093/jxb/erx295
41	帅海威，孟永杰，陈锋，等. 植物荫蔽胁迫的激素信号响应［J］. 植物学报， 2018， 53（1）： 139-148. DOI：10.11983/CBB17014. doi: 10.11983/CBB17014
42	Yang S F， Hoffman N E. Ethylene biosynthesis and its regulation in higher plants［J］. Annu Rev Plant Physiol， 1984， 35（1）： 155-189. DOI：10.1146/annurev.pp.35.060184.001103. doi: 10.1146/annurev.pp.35.060184.001103
43	刘斌. 产地、整形方式和果穗光照条件对葡萄和葡萄酒降异戊二烯产生的影响［D］. 北京：中国农业大学， 2015： 67–68.
44	曾建新. 蓝光调控拟南芥生长素生物合成、极性运输的机制和随机GFP：cDNA融合基因插入片段的克隆及功能的初步分析［D］. 长沙：湖南农业大学， 2005： 15–22.
45	Abe H， Urao T， Ito T， et al. Arabidopsis AtMYC₂ （bHLH） and AtMYB₂ （MYB） function as transcriptional activators in abscisic acid signaling［J］. Plant Cell， 2003， 15（1）： 63-78. DOI：10.1105/tpc.006130. doi: 10.1105/tpc.006130
46	Denekamp M， Smeekens S C. Integration of wounding and osmotic stress signals determines the expression of the AtMYB102 transcription factor gene［J］. Plant Physiol， 2003， 132（3）： 1415-1423. DOI：10.1104/pp.102.019273. doi: 10.1104/pp.102.019273
47	Hoeren F U， Dolferus R， Wu Y， et al. Evidence for a role for AtMYB₂ in the induction of the Arabidopsis alcohol dehydrogenase gene （ADH1） by low oxygen［J］. Genetics， 1998， 149（2）： 479-490. DOI：10.1093/genetics/149.2.479. doi: 10.1093/genetics/149.2.479
48	Quaedvlieg N， Dockx J， Keultjes G， et al. Identification of a light-regulated MYB gene from an Arabidopsis transcription factor gene collection［J］. Plant Mol Biol， 1996， 32（5）： 987-993. DOI：10.1007/bf00020495. doi: 10.1007/bf00020495
49	杨文杰，吴燕民，唐益雄. 大豆转录因子基因GmMYBJ6的表达及功能分析［J］. 遗传， 2009（6）： 645-653. DOI：10.3724/SP.J.1005.2009.00645. doi: 10.3724/SP.J.1005.2009.00645
50	岳晶，管利萍，孟思远，等. 光敏色素信号通路中磷酸化修饰研究进展［J］. 植物学报， 2015， 50： 241-254.
51	伍淑娟. 强遮荫条件下光敏色素A介导的耐荫反应机制初步研究［D］. 厦门：厦门大学， 2017： 34–57.

样本 Sample	原始序列数 Raw reads	原始碱基数 Raw bases	过滤后序列数 Clean reads	过滤后碱基数 Clean bases	有效率/% Clean_data/Raw_data	GC含量 Clean_GC_Rate/%	Q20/%	Q30 /%
齐佩华 Chippewa	446 517 054	66 977 558 100	436 965 904	65 544 885 600	97.86	35.95	96.75	92.48
矮脚早 Aijiaozao	481 894 166	72 284 124 900	470 835 464	70 625 319 600	97.71	35.99	96.78	92.58
不耐荫子代池 Shade-sensitive pool	226 579 124	33 986 868 600	220 059 398	33 008 909 700	97.12	36.13	96.53	92.21
耐荫子代池 Shade-tolerant pool	241 352 496	36 202 874 400	235 715 430	35 357 314 500	97.66	36.26	96.42	91.96

样本 Sample	过滤后序列数 Clean reads	比对上数据 Mapping reads	比对率 Mapping rate/%	优质比对率 Properly paired ratio /%	平均测序深度 Mean depth	1×覆盖度Coverage≥1× /%	5×覆盖度 Coverage≥5× /%	10×覆盖度 Coverage≥10× /%	20×覆盖度 Coverage≥20× /%
齐佩华 Chippewa	438 671 653	437 443 549	99.72	99.67	66.43	96.66	96.15	95.70	94.57
矮脚早 Aijiaozao	472 681 742	471 291 113	99.71	99.66	71.55	96.67	96.18	95.77	94.81
不耐荫子代池 Shade-sensitive pool	220 976 673	220 417 324	99.75	99.70	33.44	95.84	94.77	93.64	86.78
耐荫子代池 Shade-tolerant pool	236 607 701	234 782 375	99.23	99.17	35.64	96.05	95.12	94.13	89.01

变异位点信息 Variation sites information	齐佩华 Chippewa	矮脚早 Aijiaozao	不耐荫子代池 Shade-sensitive pool	耐荫子代池 Shade-tolerant pool
内含子Intronic	308 698	309 423	238 022	231 325
基因区间Intergenic	2 418 189	2 427 587	1 903 252	1 732 717
可变剪切位点Splicing	627	636	468	488
基因上游Upstream	186 199	187 229	141 783	137 671
基因下游Downstream	157 037	157 547	119 713	115 032
基因上游/基因下游Upstream/downstream	12 062	12 169	8 996	9 087
5’非翻译区UTR5’	22 872	22 977	17 708	17 234
3’非翻译区UTR3’	28 787	28 986	22 314	22 196
终止子提前Stop gain	1 586	1 588	1 222	1 143
终止子丢失Stop loss	255	255	198	195
同义突变Synonymous	46 852	46 917	36 819	35 892
非同义突变Non-synonymous	64 674	64 807	50 059	49 900
SNP总数SNP numbers	3 284 376	3 296 356	2 565 861	2 375 637
纯合突变SNP Hom SNP number	3 277 649	3 289 593	2 559 560	2 369 398
杂合突变SNP Hete SNP number	6 727	6 763	6 301	6 239
纯合突变SNP 比率Hom SNP rate（%）	99.80	99.79	99.75	99.74
杂合突变SNP 比率Het SNP rate（%）	0.20	0.21	0.25	0.26
转换Ts	2 127 254	2 135 306	1 656 728	1 526 282
颠换Tv	1 153 429	1 157 307	905 511	845 685
转换/颠换 Ts/Tv	1.84	1.85	1.83	1.80

[1]	Yang ZHOU, Xiao-feng YUE, Xiao-qian TANG, Hong-lin YAN, Qi ZHANG, Pei-wu LI. A preliminary study on the coupling effect of aflatoxin green control and super-nodulation [J]. CHINESE JOURNAL OF OIL CROP SCIENCES, 2021, 43(6): 947-960.
[2]	Yi-qiang HAN, Ya-mei GAO, Yan-li DU, Yu-xian ZHANG, Ji-dao DU, Wen-hui ZHANG, Shao-yu PAN. Identification of saline-alkali tolerant germplasm resources of soybean during the whole growth stage [J]. CHINESE JOURNAL OF OIL CROP SCIENCES, 2021, 43(6): 1016-1024.
[3]	Jian-qiu LIANG, Xiao-bo YU, Ze-min HE, Jian-gang AN, Jia WANG, Zhao-qiong ZENG, Wen-ying YANG, Hai-ying WU, Ming-rong ZHANG. Comparative study on the agronomic traits and yield of soybean varieties with different maturity in maize-soybean intercropping system [J]. CHINESE JOURNAL OF OIL CROP SCIENCES, 2021, 43(6): 1077-1086.
[4]	Ji-liang WANG, Chun-mei ZONG, De-liang WANG, Yan-ping WANG, Hong-xin JIANG, Dan-xia YANG, Meng-meng FU, Lei WANG, Hai-xiang REN, Tuan-jie ZHAO, Wei-guang DU, Jun-yi GAI. Identification, evaluation and improvement utilization of northeast China Soybean Germplasm Population in Jiamusi [J]. CHINESE JOURNAL OF OIL CROP SCIENCES, 2021, 43(6): 996-1005.
[5]	YANG Yong-qing, CHEN Sheng-nan, LI Xin-xin, ZHAO Qing-song, FU Ya-shu, YANG Chun-Yan, ZHANG Meng-chen, LIAO Hong. Genetic analysis and QTL mapping of soybean leaf shape under rhizobia inoculated environment [J]. CHINESE JOURNAL OF OIL CROP SCIENCES, 2021, 43(5): 825-.
[6]	XU Ying, YU Zhen-hua, LI Yan-sheng, JIN Jian, WANG Guang-hua, LIU Xiao-bing. Impact of elevated atmospheric CO₂ concentration on carbohydrate accumulation in different organs of soybean plant [J]. CHINESE JOURNAL OF OIL CROP SCIENCES, 2021, 43(5): 859-.
[7]	WANG Hua-mei, REN Chun-yuan, JIN Xi-jun, WANG Xue-meng, CAO Liang, ZHANG Ming-cong, ZHAO Qiang, YU Gao-bo, ZHANG Yu-xian . Effects of exogenous melatonin on nitrogen metabolism and growth of soybean under high nitrogen [J]. CHINESE JOURNAL OF OIL CROP SCIENCES, 2021, 43(5): 872-.
[8]	CHANG Xing-chao, WANG Xue-song, ZHANG Yan-zheng, JING Ya, CHEN Long, ZHAO Jia-liang, FANG Qing-wei, SONG Chun-xiao, LI Yong-guang, LI Wen-bin. Cloning and salt resistance analysis of soybean GmPUB32 gene [J]. CHINESE JOURNAL OF OIL CROP SCIENCES, 2021, 43(4): 638-.
[9]	LIU Ting-ting, LI Yan-yan, NING Xiao-shuang, LIU Zhi-hua, JIANG Zhen-feng, LI Wen-bin. Identification of Aux/IAA gene family and the regulation to apical bud development in soybean [J]. CHINESE JOURNAL OF OIL CROP SCIENCES, 2021, 43(4): 648-.
[10]	WANG Da-gang, CHEN Sheng-nan, YU Guo-yi, LI Jie-kun, HAN Qian-xiao, WU Qian, HU Guo-yu, HUANG Zhi-ping. Analysis on trends of main traits for summer soybean varieties released in Anhui from 1983 to 2019 [J]. CHINESE JOURNAL OF OIL CROP SCIENCES, 2021, 43(3): 510-.
[11]	DAI Yue, YAN Wei-qi, JIANG Xue, YANG Xin-yu. Establishment of a multiplex PCR for detection of four Fusarium pathogens of soybean root rot disease [J]. CHINESE JOURNAL OF OIL CROP SCIENCES, 2021, 43(2): 307-.
[12]	Isolation and identification of the fungi causing soybean seed decay in maize-soybean relay strip intercropping in Sichuan. Isolation and identification of the fungi causing soybean seed decay in maize-soybean relay strip intercropping in Sichuan [J]. CHINESE JOURNAL OF OIL CROP SCIENCES, 2021, 43(2): 314-.
[13]	ZHAO Yang, JIN Long-guo, WANG Bu-jun. Screening and detection of transgenic components in 706 conventional soybean lines [J]. CHINESE JOURNAL OF OIL CROP SCIENCES, 2021, 43(1): 117-.
[14]	LI Yun-jing, WAN Dan-feng, LIU Biao, XIAO Fang, LI Xiao-fei, WU Yu-hua, LI Jun, GAO Hong-fei, SHENG Wen-jing, LI Jun, ZHU Li, WU Gang. Research on degradation of CP4-EPSPS protein from transgenic soybean [J]. CHINESE JOURNAL OF OIL CROP SCIENCES, 2021, 43(1): 124-.
[15]	WANG Cheng, YAO Jun-jin, GAO Yue, WANG Ya-si, XIE Mei-xia, ZHAO Xin, LAN Qing-kuo, WANG Yong. Impacts of transgenic herbicide-tolerant soybean ZH10-6 with G2-EPSPS and GAT genes on field biodiversity [J]. CHINESE JOURNAL OF OIL CROP SCIENCES, 2021, 43(1): 141-.