BSA-Seq结合RNA-Seq技术挖掘大豆叶片提前黄化衰老基因

doi:10.3724/SP.J.1006.2023.34062

Abstract

Abstract:

The yield of soybean is positively correlated with the duration of reproductive growth, which delays the aging of leaves after flowering, enhances their physiological performance, and supports growing plants with heavier grains. Leaf yellowing is one of the distinctive features of plant aging. Studies on leaf yellowing at the late stage of soybean drum grain have rarely been reported. The early yellowing feature of soybean late tympanic leaves was controlled by a single recessive nuclear gene, according to the genetic analysis of the hybrid of the early yellowing mutant ly and wild-type ofc in this study. Using Molecular Marker to Map-Based Cloning, a 2.23 Mb preliminary localization interval on chromosome 19 was obtained. The interval was shortened to 1.75 Mb and contained 219 genes. When this interval was combined with RNA-Seq analysis, 12 candidate genes were detected, including 4 SNP variant genes and 8 differentially expressed genes. The findings of this study provides the framework for the cloning of genes that cause aging and yellowing during the filling later period in soybean.

Key words: soybean, mutant, BSA-Seq, RNA-Seq, map-based cloning

LI Shi-Kuan, HONG Hui-Long, FU Jia-Qi, GU Yong-Zhe, SUN Ru-Jian, QIU Li-Juan. Mine the genes of premature yellowing and aging in soybean leaves by BSA-seq combined with RNA-seq technology[J].Acta Agronomica Sinica, 2024, 50(2): 294-309.

Figures/Tables 18

Fig. 1

Table 1

Table 2

Fig. 2

Table 3

Fig. 3

Table 4

Fig. 4

Table 5

Fig. 5

Fig. 6

Table 6

Table 7

Table 8

Fig. 7

Table 9

Fig. 8

Table 10

References 57

[1]	Ainsworth E A, Yendrek C R, Skoneczka J A. Accelerating yield potential in soybean: potential targets for biotechnological improvement. Plant Cell Environ, 2012, 35: 38-52. doi: 10.1111/pce.2012.35.issue-1
[2]	Lindoo S J, Larry D N. The interrelation of fruit development and leaf senescence in Anoka soybeans. Bot Gaz, 1976, 137: 218-223. doi: 10.1086/336861
[3]	Aharoni N. Endogenous gibberellin and abscisic acid as related to senescence of detached lettuce leaves. Plant Physiol, 1978, 62: 224-228. doi: 10.1104/pp.62.2.224 pmid: 16660490
[4]	Back A, Richmond A E. Interrelations between gibberellic acid, cytokinins and abscisic acid inretarding leaf senescence. Plant Physiol, 1971, 24: 76-79. doi: 10.1111/ppl.1971.24.issue-1
[5]	Zeev E C, Itai C. The role of abscisic acid in senescence of detached tobacco leaves. Plant Physiol, 1975, 34: 97-100.
[6]	Killough D T, Horlacher W R. The inheritance of virescent yellow and red plant colors in cotton. Genetics, 1933, 18: 329-334. doi: 10.1093/genetics/18.4.329 pmid: 17246695
[7]	Huang X Q, Wang P R, Zhao H X, Deng X J. Genetic analysis and molecular mapping of a novel chlorophyll-deficit mutant gene in rice. Rice Sci, 2008, 15: 7-12. doi: 10.1016/S1672-6308(08)60013-X
[8]	Sinclair T R, Dewit C T. Analysis of the carbon and nitrogen limitations to soybean yield. Agron J, 1976, 68: 319-324. doi: 10.2134/agronj1976.00021962006800020021x
[9]	Spano G, Di F N, Perrotta C, Platani C, Ronga G, Lawlor D W, Napier J A, Shewry P R. Physiological characterization of ‘stay-green’ mutants in durum wheat. J Exp Bot, 2003, 54: 1415-1420. doi: 10.1093/jxb/erg150 pmid: 12709488
[10]	傅金民, 张庚灵, 苏芳, 王振林, 董燕, 史春余. 大豆籽粒形成期¹⁴C同化物的分配和源库调节效应的研究. 作物学报, 1999, 25: 169-173.
	Fu J M, Zhang G L, Su F, Wang Z L, Dong Y, Shi C Y. Partitioning of ¹⁴C-assimilates and effects of source-sink manipulation at seed-filling in soybean. Acta Agron Sin, 1999, 25: 169-173 (in Chinese with English abstract).
[11]	薛丽华, 章建新. 大豆鼓粒期非叶光合器官与粒重的关系. 大豆科学, 2006, 25: 425-428.
	Xue L H, Zhang J X. Relationship between non-leaf photosynthetic organs of soybean and seed weight at pod-filling date. Soybean Sci, 2006, 25: 425-428 (in Chinese with English abstract).
[12]	Lin S, Cianzio S R, Shoemaker R C. Mapping genetic loci for iron deficiency chlorosis in soybean. Mol Breed, 1997, 3: 219-229. doi: 10.1023/A:1009637320805
[13]	Palmer R G, Burzlaff J D, Shoemaker R C. Genetic analyses of two independent chlorophyll-deficient mutants identified among the progeny of a single chimeric foliage soybean plant. J Hered, 2000, 91: 297-303. pmid: 10912676
[14]	Kato K K, Palmer R G. Duplicate chlorophyll-deficient loci in soybean. Genome Biol, 2004, 47: 190-198.
[15]	崔世友, 喻德跃. 大豆不同生育时期叶绿素含量QTL的定位及其与产量的关联分析. 作物学报, 2007, 33: 744-750.
	Cui S Y, Yu D Y. QTL mapping of chlorophyll content at various growing stages and its relationship with yield in soybean. Acta Agron Sin, 2007, 33: 744-750 (in Chinese with English abstract).
[16]	Zhang H, Zhang D, Han S, Zhang X, Yu D. Identification and gene mapping of a soybean chlorophyll-deficient mutant. Plant Breed, 2011, 130: 133-138. doi: 10.1111/pbr.2011.130.issue-2
[17]	Reed S, Atkinson T, Gorecki C, Espinosa K, Przybylski S, Goggi AS, Palmer R G, Sandhu D. Candidate gene identification for a lethal chlorophyll-deficient mutant in soybean. Agron J, 2014, 4: 462-469.
[18]	陈薇. 大豆叶片黄化新突变体的表现特点与遗传研究. 南京农业大学硕士学位论文, 江苏南京, 2014.
	Chen W. Performance and Genetic Analyses of the New Yellow Leaf Mutants in Soybean. MS Thesis of Nanjing Agricultural University, Nanjing, Jiangsu, China, 2014 (in Chinese with English abstract).
[19]	冯星星. 大豆黄化突变体 Gmcdm l 与矮化突变体Gmdwf 6的基因定位. 中国科学院大学硕士学位论文, 北京, 2015.
	Feng X X. Genetic Analysis and Gene Mapping of the Gmcdm l and Gmdwf 6 in Soybean. MS Thesis of University of Chinese Academy of Sciences, Beijing, China, 2015 (in Chinese with English abstract).
[20]	Campbell B W, Mani D, Curtin S J, Slattery R A, Michno J M, Ort D R, Schaus P J, Palmer R G, Orf J H, Stupar R M. Identical substitutions in magnesium chelatase paralogs result in chlorophyll-deficient soybean mutants. G3: Genes Genom Genet, 2014, 5: 123-131.
[21]	朱晓炜. 大豆叶色突变基因GmLCM的图位克隆及功能研究. 中国科学院大学博士学位论文, 北京, 2016.
	Zhu X W. Map-based Cloning and Functional Analysis of GmLCM Associated with Soybean Leaf Color Mutant. PhD Dissertation of University of Chinese Academy of Sciences, Beijing, China, 2016 (in Chinese with English abstract).
[22]	李清. 大豆叶片黄化基因的克隆与功能分析. 中国科学院大学博士学位论文, 北京, 2016.
	Li Q. Clone and Function Analysis of the Leaf Etiolation Gene in Soybean. PhD Dissertation of University of Chinese Academy of Sciences, Beijing, China, 2016 (in Chinese with English abstract).
[23]	孔可可, 许孟歌, 王亚琪, 孔杰杰, Al-Amin G M, 赵团结. 大豆黄绿叶突变体NJ9903-5性状表现与基因定位研究. 大豆科学, 2017, 36: 494-501.
	Kong K K, Xu M G, Wang Y Q, Kong J J, Al-Amin G M, Zhao T J. Gene mapping and character performance of a yellow-green leaf mutant NJ9903-5 in soybean. Soybean Sci, 2017, 36: 494-501 (in Chinese with English abstract).
[24]	Liu M, Wang Y, Nie Z, Gai J, Bhat J A, Kong J, Zhao T. Double mutation of two homologous genes YL1 and YL2 results in a leaf yellowing phenotype in soybean [Glycine max (L.) Merr.]. Plant Mol Biol, 2020, 103: 527-543. doi: 10.1007/s11103-020-01008-9
[25]	Wang M, Li W, Fang C, Xu F, Liu Y, Wang Z, Yang R, Zhang M, Liu S, Lu S, Lin T, Tang J, Wang Y, Wang H, Lin H, Zhu B, Chen M, Kong F, Liu B, Zeng D, Jackson S A, Chu C, Tian Z. Parallel selection on a dormancy gene during domestication of crops from multiple families. Nat Genet, 2018, 50: 1435-1441. doi: 10.1038/s41588-018-0229-2 pmid: 30250128
[26]	Nawy T, Bayer M, Mravec J, Friml J, Birnbaum K D, Lukowitz W. The GATA factor HANABA TARANU is required to position the proembryo boundary in the early Arabidopsis embryo. Dev Cell, 2010, 19: 103-113. doi: 10.1016/j.devcel.2010.06.004 pmid: 20643354
[27]	Gallavotti A, Long J A, Stanfield S, Yang X, Jackson D, Vollbrecht E, Schmidt R J. The control of axillary meristem fate in the maize ramosa pathway. Development, 2010, 137: 2849-2856. doi: 10.1242/dev.051748 pmid: 20699296
[28]	Vlad D, Kierzkowski D, Rast M I, Vuolo F, Ioio R D, Galinha C, Gan X, Hajheidari M, Hay A, Smith R S, Huijser P, Bailey C D, Tsiantis M. Leaf shape evolution through duplication, regulatory diversification, and loss of a homeobox gene. Science, 2014, 343: 780-783. doi: 10.1126/science.1248384 pmid: 24531971
[29]	Stewart G C, Roeder A K, Patrick S, Chris S, Wolfgang L, Hector C. A genetic screen for mutations affecting cell division in the Arabidopsis thaliana embryo identifies seven loci required for cytokinesis. PLoS Genet, 2016, 11: e0146492.
[30]	Abe A, Kosugi S, Yoshida K, Natsume S, Takagi H, Kanzaki H, Matsumura H, Yoshida K, Mitsuoka C, Tamiru M, Innan H, Cano L, Kamoun S, Terauchi R. Genome sequencing reveals agronomically important loci in rice using MutMap. Nat Biotechnol, 2012, 30: 174-178. doi: 10.1038/nbt.2095 pmid: 22267009
[31]	Takagi H, Abe A, Yoshida K, Kosugi S, Natsume S, Mitsuoka C, Uemura A, Utsushi H, Tamiru M, Takuno S, Innan H, Cano L M, Kamoun S, Terauchi R. QTL-Seq: rapid mapping of quantitative trait loci in rice by whole genome resequencing of DNA from two bulked populations. Plant J, 2013, 74: 174-183. doi: 10.1111/tpj.2013.74.issue-1
[32]	Zhang H, Wang X, Pan Q, Li P, Liu Y, Lu X, Zhong W, Li M, Han L, Li J, Wang P, Li D, Liu Y, Li Q, Yang F, Zhang Y M, Wang G, Li L. QTL-Seq accelerates QTL fine mapping through QTL partitioning and whole-genome sequencing of bulked segregant samples. Mol Plant, 2019, 12: 426-437. doi: 10.1016/j.molp.2018.12.018
[33]	Klein H, Xiao Y, Conklin P A, Govindarajulu R, Kelly J A, Scanlon M J, Whipple C J, Bartlett M. Bulked-segregant analysis coupled to whole genome sequencing (BSA-Seq) for rapid gene cloning in maize. G3: Genes Genom Genet, 2018, 8: 3583-3592.
[34]	Lopez M H, Brinza L, Marchet C, Kielbassa J, Bastien S, Boutigny M, Monnin D, Filali A E, Carareto C M, Vieira C, Picard F, Kremer N, Vavre F, Sagot M F, Lacroix V. SNP calling from RNA-Seq data without a reference genome: identification, quantification, differential analysis and impact on the protein sequence. Nucleic Acids Res, 2016, 44: e148.
[35]	Rogier O, Chateigner A, Amanzougarene S, Lesage-Descauses M C, Balzergue S, Brunaud V, Caius J, Soubigou-Taconnat L, Jorge V, Segura V. Accuracy of RNA-seq based SNP discovery and genotyping in Populusnigra. BMC Genomics, 2018, 19: 909. doi: 10.1186/s12864-018-5239-z pmid: 30541448
[36]	Wang H, Cheng H, Wang W, Liu J, Hao M, Mei D, Zhou R, Fu L, Hu Q. Identification of BnaYucca6 as a candidate gene for branch angle in Brassica napus by QTL-Seq. Sci Rep, 2016, 6: 38493-38502. doi: 10.1038/srep38493 pmid: 27922076
[37]	Lu H, Lin T, Klein J, Wang S, Qi J, Zhou Q, Sun J, Zhang Z, Weng Y, Huang S. QTL-Seq identifies an early flowering QTL located near flowering locus T in cucumber. Theor Appl Genet, 2014, 127: 1491-1499. doi: 10.1007/s00122-014-2313-z pmid: 24845123
[38]	Lei L, Zheng H, Bi Y, Yang L, Liu H, Wang J, Sun J, Zhao H, Li X, Li J, Lai Y, Zou D. Identification of a major QTL and candidate gene analysis of salt tolerance at the bud burst stage in rice using QTL-Seq and RNA-Seq. Rice (N Y), 2020, 13: 55-68. doi: 10.1186/s12284-020-00416-1 pmid: 32778977
[39]	Song Q J, Jenkins J, Jia G F, Hyten D L, Pantalone V, Jackson S A. Construction of high resolution genetic linkage maps to improve the soybean genome sequence assembly Glyma1.01. BMC Genomics, 2016, 17: 33. doi: 10.1186/s12864-015-2344-0 pmid: 26739042
[40]	Mckenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, Depristo M A. The genome analysis toolkit: a map reduce framework for analyzing next-generation DNA sequencing data. Genome Res, 2010, 20: 1297-1303. doi: 10.1101/gr.107524.110
[41]	Cingolani P, Platts A, Wang L L, Coon M, Nguyen T, Wang L, Land S J, Lu X Y, Ruden D M. A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w¹¹¹⁸; iso-2; iso-3. Fly (Austin), 2012, 6: 80-92. doi: 10.4161/fly.19695 pmid: 22728672
[42]	Trapell C, Pacher L, Salzberg S L. Tophat: discovering splice junctions with RNA-Seq. Bionformatics, 2009, 25: 1105-1111.
[43]	Trapell C, Roberts A, Goff L, Pertea G, Kim D, Kelley D R, Pimental H, Salzberg S L, Rinn J L, Pachter L. Differential gene and transcript expression analysis of RNA-Seq experiments with TopHat and Cufflinks. Nat Protoc, 2012, 7: 562-578. doi: 10.1038/nprot.2012.016 pmid: 22383036
[44]	Benjamini Y, Yektieli D. The control of the false discovery rate in multiple testing under dependency. Ann Stat, 2001, 29: 1165-1188.
[45]	Hill J T, Demarest B L, Bisgrove B W, Gorsi B, Su Y C, Yost H J. MMAPPR: mutation mapping analysis pipeline for pooled RNA-Seq. Genome Res, 2013, 23: 687-697. doi: 10.1101/gr.146936.112 pmid: 23299975
[46]	Mckenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, DePristo M A. The genome analysis toolkit: a mapreduce framework for analyzing next-generation DNA sequencing data. Genome Res, 2010, 20: 1297-1303. doi: 10.1101/gr.107524.110 pmid: 20644199
[47]	Robinson M D, McCarthy D J, Smyth G K. EdgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics, 2010, 26, 139-140. doi: 10.1093/bioinformatics/btp616 pmid: 19910308
[48]	李得孝, 王晶, 刘修杰, 胡超, 刘义. 利用荚果厚度模拟大豆鼓粒进程的研究. 中国农业大学学报, 2014, 19(1): 29-36.
	Li D X, Wang J, Liu X J, Hu C, Liu Y. Seed-bulging simulation with pod thickness in soybean. J China Agric Univ, 2014, 19(1): 29-36 (in Chinese with English abstract).
[49]	Fraser J, Egli D B, Leggett J E. Pod and seed development in soybean cultivars with differences in seed size. Agron J, 1982, 74: 81-85. doi: 10.2134/agronj1982.00021962007400010022x
[50]	苏黎, 张仁双, 宋书宏, 董钻, 谢甫绨, 王晓光. 不同结荚习性大豆开花结荚鼓粒进程的比较研究. 大豆科学, 1997, (3): 52-59.
	Su L, Zhang R S, Song S H, Dong J, Xie F T, Wang X G. Comparative studies on flowering pod setting and seed filling of soybeans with different podding habits. Soybean Sci, 1997, (3): 52-59 (in Chinese with English abstract).
[51]	于龙凤, 孙海桥, 安福全. 不同大豆品种叶片叶绿素变化规律的研究. 黑龙江农业科学, 2009, (2): 32-34.
	Yu L F, Sun H Q, An F Q. Study on leaf blade chlorophyll change of different soybean varieties. Heilongjiang Agric Sci, 2009, (2): 32-34 (in Chinese with English abstract).
[52]	王聪, 赵连佳, 张建勋, 章建新. 春大豆鼓粒期冠层翻叶原因及翻叶对叶片净光合速率和粒重的影响. 中国农学通报, 2020, 36(33): 38-44. doi: 10.11924/j.issn.1000-6850.casb20191200926
	Wang C, Zhao L J, Zhang J X, Zhang J X. Canopy leaf turning of spring soybean at seed-filling stage: reasons and effects on net photosynthetic rate and grain weight. Chin Agric Sci Bull, 2020, 36(33): 38-44 (in Chinese with English abstract). doi: 10.11924/j.issn.1000-6850.casb20191200926
[53]	杨阳, 苍晶, 王学东, 崔琳, 王兴, 周子珊. 大豆豆荚光合特性及其对产量的贡献. 东北农业大学学报, 2008, 39(12): 51-56.
	Yang Y, Cang J, Wang X D, Cui L, Wang X, Zhou Z S. Photosynthetic characteristics of soybean pod and its contribution to yield. J Northeast Agric Univ, 2008, 39(12): 51-56 (in Chinese with English abstract).
[54]	林国强, 黄建成, 徐树传, 王金官. 菜用大豆“292”秋播花后干物质积累及鼓粒特性的研究. 大豆科学, 1997, 16: 293-297.
	Lin G Q, Huang J C, Xu S C, Wang J G. Studies on dry matter accumulation and seed filling characteristics after anthesis in fall of vegetable soybean 292. Soybean Sci, 1997, 16: 293-297 (in Chinese with English abstract).
[55]	Kavakli I H, Slattery C J, Ito H, Okita T W. The conversion of carbon and nitrogen into starch and storage proteins in developing storage organs: an overview. Funct Plant Biol, 2000, 27: 561-570. doi: 10.1071/PP99176
[56]	郎漫, 刘元英, 彭显龙, 张文钊. 不同氮肥用量下镁对大豆碳氮代谢的影响. 大豆科学, 2006, 25: 49-52.
	Lang M, Liu Y Y, Peng X L, Zhang W Z. Effects of magnesium on carbon and nitrogen metabolism of soybean at different effects of magnesium on carbon and nitrogen metabolism of soybean at different. Soybean Sci, 2006, 25: 49-52 (in Chinese with English abstract).
[57]	李菁华, 张明聪, 金喜军, 王孟雪, 任春元, 张玉先, 胡国华, 宋晓慧. 高油型和高蛋白型大豆鼓粒期的糖分积累规律. 大豆科学, 2017, 36: 68-73.
	Li J H, Zhang M C, Jin X J, Wang M X, Ren C Y, Zhang Y X, Hu G H, Song X H. Sugar accumulation rule of high oil and high protein soybean during the seed-filling period. Soybean Sci, 2017, 36: 68-73 (in Chinese with English abstract).

Metrics

Viewed

Full text

Abstract

Cited

Shared

Discussed

Comments

Recommended 10

[1]	Li Shaoqing, Li Yangsheng, Wu Fushun, Liao Jianglin, Li Damo. Optimum Fertilization and Its Corresponding Mechanism under Complete Submergence at Booting Stage in Rice[J]. Acta Agronomica Sinica, 2002, 28(01): 115 -120 .
[2]	Wang Lanzhen;Mi Guohua;Chen Fanjun;Zhang Fusuo. Response to Phosphorus Deficiency of Two Winter Wheat Cultivars with Different Yield Components[J]. Acta Agron Sin, 2003, 29(06): 867 -870 .
[3]	YANG Jian-Chang;ZHANG Jian-Hua;WANG Zhi-Qin;ZH0U Qing-Sen. Changes in Contents of Polyamines in the Flag Leaf and Their Relationship with Drought-resistance of Rice Cultivars under Water Deficiency Stress[J]. Acta Agron Sin, 2004, 30(11): 1069 -1075 .
[4]	Yan Mei;Yang Guangsheng;Fu Tingdong;Yan Hongyan. Studies on the Ecotypical Male Sterile-fertile Line of Brassica napus L.Ⅲ. Sensitivity to Temperature of 8-8112AB and Its Inheritance[J]. Acta Agron Sin, 2003, 29(03): 330 -335 .
[5]	Wang Yongsheng;Wang Jing;Duan Jingya;Wang Jinfa;Liu Liangshi. Isolation and Genetic Research of a Dwarf Tiilering Mutant Rice[J]. Acta Agron Sin, 2002, 28(02): 235 -239 .
[6]	WANG Li-Yan;ZHAO Ke-Fu. Some Physiological Response of Zea mays under Salt-stress[J]. Acta Agron Sin, 2005, 31(02): 264 -268 .
[7]	TIAN Meng-Liang;HUNAG Yu-Bi;TAN Gong-Xie;LIU Yong-Jian;RONG Ting-Zhao. Sequence Polymorphism of waxy Genes in Landraces of Waxy Maize from Southwest China[J]. Acta Agron Sin, 2008, 34(05): 729 -736 .
[8]	HU Xi-Yuan;LI Jian-Ping;SONG Xi-Fang. Efficiency of Spatial Statistical Analysis in Superior Genotype Selection of Plant Breeding[J]. Acta Agron Sin, 2008, 34(03): 412 -417 .
[9]	WANG Yan;QIU Li-Ming;XIE Wen-Juan;HUANG Wei;YE Feng;ZHANG Fu-Chun;MA Ji. Cold Tolerance of Transgenic Tobacco Carrying Gene Encoding Insect Antifreeze Protein[J]. Acta Agron Sin, 2008, 34(03): 397 -402 .
[10]	ZHENG Xi;WU Jian-Guo;LOU Xiang-Yang;XU Hai-Ming;SHI Chun-Hai. Mapping and Analysis of QTLs on Maternal and Endosperm Genomes for Histidine and Arginine in Rice (Oryza sativa L.) across Environments[J]. Acta Agron Sin, 2008, 34(03): 369 -375 .

引物名称 Primer name	上游引物序列 Forward primer (5°-3°)	下游引物序列 Reverse primers (5°-3°)
Glyma.19G223400	TGATTGGTTTAGCCGTGTTTC	AACATCTCGGTTGTAAGTCCTCT
Glyma.19G228000	ATGTAACAGAAGGACGCG	TGTTGGTAAATAGAGTAATG
Glyma.19G236800	TAACATCACTCAAATAAAAC	AACCAGCTTAACAACCTCAA
Glyma.19G237000	AGAAGACATGGTTCCAGCAC	CCCGAGGAATCTCAAAGGA
Glyma.19G216000	CACTTTGCTTTCTTCTCCCTT	TACCAGCATTGATGCAGTTT
Glyma.19G233000	AATAGCCATTTCGCTTATC	ACAAACTTGTTGGGAGTAG
Glyma.19G219600	AGTAGTATAGAAGTGCGTAA	CTTCTCAACTACTTATTAAGATATG
Glyma.19G241500D	ATGCGTATGGACTTCCCCAA	TGGCATTCGTTGGGCACTAA

引物名称 Primer ID	上游引物序列 Forward primer (5°-3°)	下游引物序列 Reverse primers (5°-3°)
216000	Fam: GAAGGTGACCAAGTTCATGCTTGGAGGGAGGGGGACTGg Hex: GAAGGTCGGAGTCAACGGATTGTGGAGGGAGGGGGACTGa	ACTTTGCTTTCTTCTCCCTTTTATCTTTCT
223400	Fam: GAAGGTGACCAAGTTCATGCTATAGGACCATTAAGAGGCGGCATt Hex: GAAGGTCGGAGTCAACGGATTTAGGACCATTAAGAGGCGGCATc	AAGACAGATGCTGCAGCTGCG
228000	Fam: GAAGGTGACCAAGTTCATGCTCGCCGAAATATAGTCACCGg Hex: GAAGGTCGGAGTCAACGGATTAACGCCGAAATATAGTCACCGa	CTGAGATTCGGAGAAGCTTGC
219600	Fam: GAAGGTGACCAAGTTCATGCTGGTGTCAATTTTCTAAAAATTCATACTCTTc Hex: GAAGGTCGGAGTCAACGGATTGGTGTCAATTTTCTAAAAATTCATACTCTTt	TTGTGACTTTCTCTTCTCAACTACTTATTAAG
233000	Fam: GAAGGTGACCAAGTTCATGCTATAAGTTCTTCAGTGTTCACTTGAGAGg Hex: GAAGGTCGGAGTCAACGGATTAATAAGTTCTTCAGTGTTCACTTGAGAGa	TCATTAGTCCTTAACCCGTCACATAG
237000	Fam: GAAGGTGACCAAGTTCATGCTATGCATCACGGGTCATTCTg Hex: GAAGGTCGGAGTCAACGGATTAAATGCATCACGGGTCATTCTa	CAAAGAAAGAAAGTAACTACTGAAGTGTACG
241500D	ATGCGTATGGACTTCCCCAA	ATCAGTTTTGTAAATAATAGTTGTgA

取样时间 Time	(种子鲜重-种子干重)/荚果重 (Seed fresh weight-Seed dry weight)/Pod weight			种子干重/荚果重 Seed dry weight/Pod weight
取样时间 Time	野生型 Wild-type	突变型 Mutant	t检验的P值 P-value by t-test	野生型 Wild-type	突变型 Mutant	t检验的P值 P-value by t-test
第1天Day 1	0.31	0.31	P=0.91	0.24	0.28	P=0.04<0.05
第2天Day 2	0.31	0.31		0.26	0.29
第3天Day 3	0.29	0.31		0.28	0.30
第4天Day 4	0.34	0.35		0.26	0.30
第5天Day 5	0.34	0.34		0.33	0.31
第6天Day 6	0.35	0.34		0.35	0.34
第7天Day 7	0.36	0.34		0.35	0.39
第8天Day 8	0.22	0.23		0.50	0.52

生长条件 Growth conditions	性状 Characters		株高 Plant height (cm)	分枝 Branch	节数 Number of sections	荚数 Number of pods	粒数 Number of grains	百粒重 100-grain weight (g)
短日照条件 Short-day conditions	矮皱叶 Dwarf-wrink led leaves	野生型 Wild	34.32±3.98^*	0.37±0.51	12.75±1.42	27.36±7.33^*	42.93±14.08^*	34.81±4.18^**
	矮皱叶 Dwarf-wrink led leaves	突变型 Mutant	29.31±3.45^*	0.27±0.53	11.07±1.93	22.34±10.58^*	37.18±18.32^*	29.44±2.21^**
	高展叶 Tall-flat leaves	突变型 Mutant	45.28±6.20^**	1.52±1.72^*	11.91±1.26^*	32.06±16.13	61.96±31.66	30.72±3.14^**
	高展叶 Tall-flat leaves	野生型 Wild	52.32±5.02^**	0.77±1.14^*	13.32±1.65^*	32.75±14.60	65.55±34.33	37.44±3.51^**
长日照条件 Long-day conditions	矮皱叶 Dwarf-wrink led leaves	野生型 Wild	65.66±7.52	0.44±0.42	19.51±2.47	35.97±10.02^*	51.37±13.93	27.74±1.50
	矮皱叶 Dwarf-wrink led leaves	突变型 Mutant	67.30±7.38	0.55±0.40	21.71±1.05	42.89±9.42^*	51.27±6.29	27.32±1.20
	高展叶 Tall-flat leaves	突变型 Mutant	122.15±6.23	4.31±1.11^*	23.26±0.95	114.50±25.84	194.39±51.06^*	33.62±1.82^**
	高展叶 Tall-flat leaves	野生型 Wild	124.79±9.12	2.95±1.06^*	22.67±1.32	85.81±17.37	173.87±29.41^*	37.42±1.72^**

关联分析类型 Association analysis type	染色体 Chr.	起始位置 Start position	终止位置 Termination location	区间大小 Region size (Mb)	区间内基因数量 Gene number in the regions
SNP关联结果SNP correlates results	Chr19	45760000	50720000	4.96	636
InDel关联结果InDel correlates results	Chr11	0	250000	0.25	44
	Chr05	20110000	21450000	1.34	10
	Chr12	16090000	16560000	0.47	16
	Chr16	21180000	23610000	2.43	51
	Chr17	24150000	25190000	1.04	12
	Chr17	35420000	35660000	0.24	2
	Chr18	26340000	26470000	0.13	3
	Chr18	9180000	9390000	0.21	15
	Chr19	46440000	49040000	2.60	326
2个关联结果交集 The intersection of the two association results	Chr19	46810000	49040000	2.23	277

Mine the genes of premature yellowing and aging in soybean leaves by BSA-seq combined with RNA-seq technology

RichHTML420

PDF

Abstract

Cite this article

share this article

Figures/Tables 18

References 57

Related Articles 15

Metrics

Comments

Recommended 10

值 Value	表型 Phenotype	基因型 Genotype	标记Marker
值 Value	表型 Phenotype	基因型 Genotype	216000	219600	223400	228000	233000	237000	241500D
理论值 Theoretical value	绿色Green	A	197	195	259	197	180	197	214
理论值 Theoretical value	黄色Yellow	B	149	196	183	194	183	149	163
实际值 Actual value	绿色Green	A	67	182	181	257	176	171	145
实际值 Actual value	黄色Yellow	B	115	119	193	166	189	176	102
χ²值χ²-value			31.13	6.91	0.97	1.50	2.24	0.63	22.25
P值P-value			0	0.01	0.31	0.21	0.12	0.40	0

基因ID Gene ID	SNP位点 SNP loci	碱基类型 Base type		突变类型 Mutation type	突变的影响 Effects of mutations
基因ID Gene ID	SNP位点 SNP loci	野生型 Wild type	突变型 Mutant	突变类型 Mutation type	突变的影响 Effects of mutations
Glyma.19G223400	47582632	A	G	基因的3'UTR内 Gene within 3' UTR	改变RNA二级结构 Change the RNA secondary structure
Glyma.19G233000	48299560	A	G	基因的3'UTR内 Gene within 3' UTR	改变RNA二级结构 Change the RNA secondary structure
Glyma.19G236800	48581005	A	G	非同义SNV Non-synonymous SNV	脯氨酸变成亮氨酸, 改变蛋白结构 Proline becomes leucine, changing the protein structure
Glyma.19G237000	48622649	T	C	基因的5'UTR内 Gene within 5' UTR	改变RNA二级结构 Change the RNA secondary structure

基因编号 Gene number	野生型子代FPKM值 Wild type offspring FPKM value	突变型子代FPKM值 Mutant offspring FPKM value	野生型亲本FPKM值 FPKM values of wild type parents	突变型亲本FPKM值 FPKM values of mutant parents	野生型vs突变型 Wild type vs mutant
Glyma.19G223400	5.97	8.20	6.65	7.87	no
Glyma.19G233000	15.50	17.41	15.19	14.89	no
Glyma.19G236800	22.14	14.91	19.63	19.63	no
Glyma.19G237000	2.35	4.24	1.97	2.89	no

基因编号 Gene number	野生型子代FPKM值 Wild type offspring FPKM value	突变型子代FPKM值 Mutant offspring FPKM value	野生型亲本FPKM值 FPKM values of wild type parents	突变型亲本FPKM值 FPKM values of mutant parents	野生型vs突变型 Wild type vs mutant
Glyma.19G222400	1.141	0.311	1.959	0.334	up
Glyma.19G224500	2.857	15.923	1.933	10.123	down
Glyma.19G225900	0.446	0.083	0.959	0.039	up
Glyma.19G226800	14.965	3.935	11.658	2.708	up
Glyma.19G228200	1.935	0.051	1.032	0.200	up
Glyma.19G228300	4.934	0.775	4.272	0.751	up
Glyma.19G230600	1.125	0.470	1.485	0.329	down
Glyma.19G241200	59.422	137.849	45.382	103.845	down

类型 Type	基因编号 Gene number	具有同源序列的蛋白 Proteins with homologous sequences
SNP突变 SNP mutations	Glyma.19G223400	G蛋白β亚基(含WD40重复蛋白同源序列)、丝氨酸/苏氨酸激酶受体相关蛋白以及醌血红素蛋白β亚基 G protein β subunits (containing WD40 repeat homologous sequences), serine/threonine kinase receptor-associated proteins, and quinone heme protein β subunits
	Glyma.19G233000	乙酰肝素-α-氨基葡萄糖苷N-乙酰转移酶Heparan-α-glucosaside N-acetyltransferase
	Glyma.19G236800	E3泛素蛋白连接酶、和锌指结构域 E3 ubiquitin protein ligase, and zinc finger domains
	Glyma.19G237000	PLP依赖的D-天冬氨酸氨基转移酶, 核苷三磷酸水解酶的P环 PLP-dependent D-aspartate aminotransferase, the P loop of nucleoside triphosphate hydrolases
差异表达基因 Differentially expressed genes	Glyma.19G222400	果胶乙酰酯酶家族蛋白Pectin acetylesterase family proteins
	Glyma.19G224500	果胶乙酰酯酶家族蛋白Pectin acetylesterase family proteins
	Glyma.19G225900	碳水化合物代谢过程碳水化合物结合X8结构域蛋白 Carbohydrate metabolism process, carbohydrate binding to X8 domain protein
	Glyma.19G226800	核苷三磷酸水解酶的P环P loop of nucleoside triphosphate hydrolases
	Glyma.19G228200	类似ECH相关蛋白1的Kelch Kelch-like ech-associated protein 1
	Glyma.19G228300	转录因子MEIS1和相关HOX结构域蛋白 Transcription factor MEIS1 and associated HOX-domain proteins
	Glyma.19G230600	丝氨酸/苏氨酸特异性蛋白磷酸酶, 蛋白磷酸酶2C Serine/threonine-specific protein phosphatase, protein phosphatase 2C
	Glyma.19G241200	转移酶活性, 转移氨基酰基以外的酰基 Transferase activity, transfer of acyl groups other than aminoacyl

[1]	WANG Qiong, ZHU Yu-Xiang, ZHOU Mi-Mi, ZHANG Wei, ZHANG Hong-Mei, CEHN Xin, CEHN Hua-Tao, CUI Xiao-Yan. Genome-wide association analysis and candidate genes predication of leaf characteristics traits in soybean (Glycine max L.) [J]. Acta Agronomica Sinica, 2024, 50(3): 623-632.
[2]	LIU Wei, WANG Yu-Bin, LI Wei, ZHANG Li-Feng, XU Ran, WANG Cai-Jie, ZHANG Yan-Wei. Overexpression of soybean isopropyl malate dehydrogenase gene GmIPMDH promotes flowering and growth [J]. Acta Agronomica Sinica, 2024, 50(3): 613-622.
[3]	SONG Jian, XIONG Ya-Jun, CHEN Yi-Jie, XU Rui-Xin, LIU Kang-Lin, GUO Qing-Yuan, HONG Hui-Long, GAO Hua-Wei, GU Yong-Zhe, ZHANG Li-Juan, GUO Yong, YAN Zhe, LIU Zhang-Xiong, GUAN Rong-Xia, LI Ying-Hui, WANG Xiao-Bo, GUO Bing-Fu, SUN Ru-Jian, YAN Long, WANG Hao-Rang, JI Yue-Mei, CHANG Ru-Zhen, WANG Jun, QIU Li-Juan. Genetic analysis of seed coat and flower color based on a soybean nested association mapping population [J]. Acta Agronomica Sinica, 2024, 50(3): 556-575.
[4]	YANG Chuang, WANG Ling, QUAN Cheng-Tao, YU Liang-Qian, DAI Cheng, GUO Liang, FU Ting-Dong, MA Chao-Zhi. Relative expression profiles of genes response to salt stress and constructions of gene co-expression networks in Brassica napus L. [J]. Acta Agronomica Sinica, 2024, 50(1): 237-250.
[5]	YANG Li-Da, REN Jun-Bo, PENG Xin-Yue, YANG Xue-Li, LUO Kai, CHEN Ping, YUAN Xiao-Ting, PU Tian, YONG Tai-Wen, YANG Wen-Yu. Crop growth characteristics and its effects on yield formation through nitrogen application and interspecific distance in soybean/maize strip relay intercropping [J]. Acta Agronomica Sinica, 2024, 50(1): 251-264.
[6]	SHI Yu-Xin, LIU Xin-Yue, SUN Jian-Qiang, LI Xiao-Fei, GUO Xiao-Yang, ZHOU Ya, QIU Li-Juan. Knockout of GmBADH1 gene using CRISPR/Cas9 technique to reduce salt tolerance in soybean [J]. Acta Agronomica Sinica, 2024, 50(1): 100-109.
[7]	YUAN Xiao-Ting, WANG Tian, LUO Kai, LIU Shan-Shan, PENG Xin-Yue, YANG Li-Da, PU Tian, WANG Xiao-Chun, YANG Wen-Yu, YONG Tai-Wen. Effects of bandwidth and plant spacing on biomass accumulation and allocation and yield formation in strip intercropping soybean [J]. Acta Agronomica Sinica, 2024, 50(1): 161-171.
[8]	HU Xin, LUO Zheng-Ying, LI Chun-Jia, WU Zhuan-Di, LI Xu-Juan, LIU Xin-Long. Comparative transcriptome analysis of elite ‘ROC’ sugarcane parents for exploring genes involved in Sporisorium scitamineum infection by using Illumina- and SMRT-based RNA-seq [J]. Acta Agronomica Sinica, 2023, 49(9): 2412-2432.
[9]	WANG Juan, XU Xiang-Bo, ZHANG Mao-Lin, LIU Tie-Shan, XU Qian, DONG Rui, LIU Chun-Xiao, GUAN Hai-Ying, LIU Qiang, WANG Li-Ming, HE Chun-Mei. Characterization and genetic analysis of a new allelic mutant of Miniature1 gene in maize [J]. Acta Agronomica Sinica, 2023, 49(8): 2088-2096.
[10]	SU Zai-Xing, HUANG Zhong-Qin, GAO Run-Fei, ZHU Xue-Cheng, WANG Bo, CHANG Yong, LI Xiao-Shan, DING Zhen-Qian, YI Yuan. Identification of wheat dwarf mutant Xu1801 and analysis of its dwarfing effect [J]. Acta Agronomica Sinica, 2023, 49(8): 2133-2143.
[11]	LI Gang, ZHOU Yan-Chen, XIONG Ya-Jun, CHEN Yi-Jie, GUO Qing-Yuan, GAO Jie, SONG Jian, WANG Jun, LI Ying-Hui, QIU Li-Juan. Haplotype analysis of soybean leaf type regulator gene Ln and its homologous genes [J]. Acta Agronomica Sinica, 2023, 49(8): 2051-2063.
[12]	LIU Ting-Xuan, GU Yong-Zhe, ZHANG Zhi-Hao, WANG Jun, SUN Jun-Ming, QIU Li-Juan. Mapping soybean protein QTLs based on high-density genetic map [J]. Acta Agronomica Sinica, 2023, 49(6): 1532-1541.
[13]	DAI Wen-Hui, ZHU Qi, ZHANG Xiao-Fang, LYU Shen-Yang, XIANG Xian-Bo, MA Tao, CHEN Yu-Jie, ZHU Shi-Hua, DING Wo-Na. Identification and gene mapping of brittle culm mutant bc21 in rice [J]. Acta Agronomica Sinica, 2023, 49(5): 1426-1431.
[14]	LI Hui, LU Yi-Ping, WANG Xiao-Kai, WANG Lu-Yao, QIU Ting-Ting, ZHANG Xue-Ting, HUANG Hai-Yan, CUI Xiao-Yu. GmCIPK10, a CBL-interacting protein kinase promotes salt tolerance in soybean [J]. Acta Agronomica Sinica, 2023, 49(5): 1272-1281.
[15]	YAN Xin, XIANG Chao, LIU Rong, LI Guan, LI Meng-Wei, LI Zheng-Li, ZONG Xu-Xiao, YANG Tao. Fine mapping of flower colour gene in pea (Pisum sativum L.) based on BSA-seq technique [J]. Acta Agronomica Sinica, 2023, 49(4): 1006-1015.