大豆红色种皮的色素鉴定和基因定位

doi:10.3864/j.issn.0578-1752.2023.14.002

Abstract

Abstract:

【Objective】To identify the key genes controlling anthocyanin synthesis and accumulation, to uncover changes in anthocyanin content of the seed coat during seed development, and the primary anthocyanin components responsible for the red seed coat of Taixingaijiaohong (TXAJH); and to lay the groundwork for a thorough understanding of the regulatory mechanism of red seed coat formation.【Method】Using ultra-high performance liquid chromatography-tandem mass spectrometry (UPLC-ESI-MS/MS), the anthocyanin composition and concentration of the yellow seed coat of soybean Suinong 14 (SN14) and the red seed coat of soybean TXAJH at various developmental stages were identified. The potential areas of red testa-related genes were first identified using bulked segregant analysis (BSA) on the recombinant inbred lines (RILs) made by crossing SN14 and TXAJH. Based on this discovery, we performed marker linkage analysis to restrict the candidate intervals and predict the candidate genes, and qRT-PCR to confirm the expression of the anticipated candidate genes.【Result】When seed coats from the four developmental phases of SN14 and TXAJH were analyzed, a total of 12 anthocyanins were discovered. Cluster analysis of total anthocyanins revealed substantial changes in the seed coat's anthocyanin composition between TXAJH and SN14 as well as between TXAJH before and after color development. The anthocyanin content of the SN14 seed coat gradually decreased as the seed developed, whereas the TXAJH seed coat's content increased quickly and remained stable. After the development of the seed coat's color, the anthocyanin contents of SN14 and TXAJH showed highly significant differences, and at the mature stage, the TXAJH seed coat's anthocyanin content was more than 200 times that of SN14. The crimson coloring of the TXAJH seed coat was largely due to cyanidin-3-O-glucoside (Cy-3-glu), peonidin-3-O-glucoside (Pn-3-glu), and petunidin-3-O-glucoside (Pt-3-glu). The candidate interval for the red seed coat gene on chromosome 8 was discovered at 8.66 Mb by BSA-seq association analysis. 27 polymorphic markers were used in the marker linkage analysis, which produced 10 haplotypes and reduced the candidate interval to 702 kb. Nonsynonymous variations in 37 genes between the parents were found during this interval, these include the genes for encode the anthocyanin reductase 1 (Glyma.08g062000), the bHLH transcription factor (Glyma.08g061300 and Glyma.08g063900), and the MYB transcript factor (Glyma.08g059900). These genes may be involved in regulating the biosynthesis of anthocyanins, and anthocyanin reductase 1 can convert anthocyanins to proanthocyanidins (PA). The results of gene expression analysis revealed that candidate genes and genes related to the anthocyanin biosynthesis pathway had comparable expression patterns in SN14 and TXAJH, and both were expressed at lower levels in SN14 and at higher levels in TXAJH. It was discovered that there was a significant link between the principal constituents of seed coat anthocyanins and the level of candidate gene expression.【Conclusion】The anthocyanin makeup of SN14 and TXAJH's seed coats differed, and Cy-3-glu, Pn-3-glu, and Pt-3-glu may be to blame for the TXAJH's seed coat's red hue. According to predictions, Glyma.08g059900, Glyma.08g061300, Glyma.08g062000, and Glyma.08g063900 will likely be a candidate gene for the red seed coat, in which Glyma.08g059900, Glyma.08g061300, and Glyma.08g063900 may control a number of anthocyanin biosynthesis pathway genes.

Key words: soybean, seed coat color, anthocyanin, BSA-seq, gene mapping

CAO Jie, GU YongZhe, HONG HuiLong, WU HaiTao, ZHANG Xia, SUN JianQiang, BAO LiGao, QIU LiJuan. Pigment Identification and Gene Mapping in Red Seed Coat of Soybean[J].Scientia Agricultura Sinica, 2023, 56(14): 2643-2659.

Figures/Tables 10

Fig. 1

Fig. 2

Table 1

Table 2

Fig. 3

Fig. 4

Table 3

Fig. 5

Table 4

Candidate interval genes and functional notes"

基因编号 Gene ID	位置 Location (bp)	功能注释 Function
Glyma.08g058100	Chr.08: 4460549-4465659	单链核糖核酸内切酶Single-stranded-nucleate endonuclease
Glyma.08g059300	Chr.08: 4530151-4536884	吡啶核苷酸-二硫化物氧化还原酶Pyridine nucleotide-disulphide oxidoreductase
Glyma.08g059800	Chr.08: 4601723-4608768	囊泡相关蛋白Vesicle-associated protein
Glyma.08g059900	Chr.08: 4616457-4618234	MYB转录因子MYB transcription factor
Glyma.08g060400	Chr.08: 4648226-4658991	PLAC8蛋白家族PLAC8 family
Glyma.08g060500	Chr.08: 4664282-4669458	酪氨酸蛋白激酶Tyrosine protein kinase
Glyma.08g060600	Chr.08: 4673233-4676958	含五肽重复的蛋白质Proteins containing pentapeptide repeats
Glyma.08g060800	Chr.08: 4681172-4690671	苏氨酸激酶Threonine kinase
Glyma.08g060900	Chr.08: 4691761-4694059	苏氨酸蛋白激酶Threonine-protein kinase
Glyma.08g061000	Chr.08: 4694260-4698526	酪氨酸蛋白激酶Tyrosine protein kinase
Glyma.08g061100	Chr.08: 4708531-4710950	含U-BOX结构域的蛋白质8 U-box domain-containing protein 8
Glyma.08g061200	Chr.08: 4718616-4721895	NAD(P)H脱氢酶NAD(P)H dehydrogenase
Glyma.08g061300	Chr.08: 4731510-4735504	bHLH转录因子bHLH transcription factor
Glyma.08g061500	Chr.08: 4745228-4747004	PPR重复系列PPR repeat
Glyma.08g061600	Chr.08: 4751073-4754299	橙花醇合酶Nerolidol synthase
Glyma.08g062000	Chr.08: 4783724-4786913	花青素还原酶1 Anthocyanidin reductase 1
Glyma.08g062400	Chr.08: 4805184-4806757	--
Glyma.08g062500	Chr.08: 4809724-4816932	驱动蛋白Kinesin
Glyma.08g062600	Chr.08: 4817430-4821371	安全家族蛋白Safe family protein
Glyma.08g062700	Chr.08: 4829862-4832511	酪氨酸蛋白激酶Tyrosine protein kinase
Glyma.08g062800	Chr.08: 4833755-4836533	苏氨酸蛋白激酶Threonine-protein kinase
Glyma.08g062900	Chr.08: 4837205-4840140	酪氨酸蛋白激酶Tyrosine protein kinase
Glyma.08g063200	Chr.08: 4848292-4850826	蛋氨酸转氨酶Methionine transaminase
Glyma.08g063300	Chr.08: 4851595-4856852	蛋氨酸转氨酶Methionine transaminase
Glyma.08g063600	Chr.08: 4883287-4887296	MuDR家族转座酶MuDR family transposase
Glyma.08g063700	Chr.08: 4888519-4892619	角鲨烯单加氧酶Squalene monooxygenase
Glyma.08g063800	Chr.08: 4897354-4900790	L-苹果酸脱氢酶L-Malate dehydrogenase
Glyma.08g063900	Chr.08: 4905921-4906926	bHLH转录因子bHLH transcription factor
Glyma.08g064000	Chr.08: 4910549-4911502	--
Glyma.08g064200	Chr.08: 4915590-4916430	--
Glyma.08g064300	Chr.08: 4917314-4927545	蛋白质S-酰基转移酶Protein S-acyltransferase
Glyma.08g064400	Chr.08: 4927906-4929447	--
Glyma.08g064500	Chr.08: 4932437-4940287	鞘脂转运蛋白同源物Sphingolipid transporter spinster homolog
Glyma.08g064600	Chr.08: 4943335-4953605	K⁺外向逆流转运蛋白K⁺ efflux antiporter
Glyma.08g064700	Chr.08: 4956340-4959142	鸟氨酸环脱氨酶相关Ornithine cyclodeaminase-related
Glyma.08g064800	Chr.08: 4963573-4966706	蛋白质毛状体双折射Protein trichome birefringence-like
Glyma.08g065000	Chr.08: 4977696-4979377	PB1域PB1 domain

Table 4

Fig. 6

References 70

[1]	GUO B F, SUN L P, JIANG S Q, REN H L, SUN R J, WEI Z Y, HONG H L, LUAN X Y, WANG J, WANG X B, XU D H, LI W B, GUO C H, QIU L J. Soybean genetic resources contributing to sustainable protein production. Theoretical and Applied Genetics, 2022, 135(11): 4095-4121. doi: 10.1007/s00122-022-04222-9 pmid: 36239765
[2]	FANG C, KONG F J. Soybean. Current Biolog, 2022, 32(17): R902-R904.
[3]	宋健. 大豆种皮色相关基因的图位克隆及功能解析[D]. 北京: 中国农业科学院, 2019.
	SONG J. Mapping cloning and functional analysis of genes relatead to oybean seed coat color[D]. Beijing: Chinese Academy of Agricultural Sciences, 2019. (in Chinese)
[4]	KOVINICH N, SALEEM A, RINTOUL T L, BROWN D C W, ARNASON J T, MIKI B. Coloring genetically modified soybean grains with anthocyanins by suppression of the proanthocyanidin genes ANR1 and ANR2. Transgenic Research, 2012, 21(4): 757-771. doi: 10.1007/s11248-011-9566-y
[5]	ENARU B, DREȚCANU G, POP T D, STǍNILǍ A, DIACONEASA Z. Anthocyanins: Factors affecting their stability and degradation. Antioxidants, 2021, 10(12): 1967. doi: 10.3390/antiox10121967
[6]	POJER E, MATTIVI F, JOHNSON D, STOCKLEY C S. The case for anthocyanin consumption to promote human health: A review. Comprehensive Reviews in Food Science and Food Safety, 2013, 12(5): 483-508. doi: 10.1111/crf3.2013.12.issue-5
[7]	LEE Y M, YOON Y, YOON H, PARK H M, SONG S, YEUM K J. Dietary anthocyanins against obesity and inflammation. Nutrients, 2017, 9(10): 1089. doi: 10.3390/nu9101089
[8]	MATTIOLI R, FRANCIOSO A, MOSCA L, SILVA P. Anthocyanins: a comprehensive review of their chemical properties and health effects on cardiovascular and neurodegenerative diseases. Molecules, 2020, 25(17): 3809. doi: 10.3390/molecules25173809
[9]	LIU J Q, ZHOU H B, SONG L, YANG Z J, QIU M, WANG J, SHI S L. Anthocyanins: Promising natural products with diverse pharmacological activities. Molecules, 2021, 26(13): 3807. doi: 10.3390/molecules26133807
[10]	NOMI Y, IWASAKI-KURASHIGE K, MATSUMOTO H, TSUDA T, KALT W. Therapeutic effects of anthocyanins for vision and eye health. Molecules, 2019, 24(18): 3311. doi: 10.3390/molecules24183311
[11]	NGAMSAMER C, SIRIVARASAI J, SUTJARIT N. The benefits of anthocyanins against obesity-induced inflammation. Biomolecules, 2022, 12(6): 852. doi: 10.3390/biom12060852
[12]	DE ARRUDA NASCIMENTO E,DE LIMA COUTINHO L, DA SILVA C J, DE LIMA V L A G, DOS SANTOS AGUIAR J. In vitro anticancer properties of anthocyanins: A systematic review. Biochimica et Biophysica Acta Reviews on Cancer, 2022, 1877(4): 188748. doi: 10.1016/j.bbcan.2022.188748
[13]	NAING A H, KIM C K. Abiotic stress-induced anthocyanins in plants: Their role in tolerance to abiotic stresses. Physiologia Plantarum, 2021, 172(3): 1711-1723. doi: 10.1111/ppl.v172.3
[14]	ZHANG Q L, ZHAI J J, SHAO L, LIN W, PENG C L. Accumulation of anthocyanins: an adaptation strategy of Mikania micrantha to low temperature in winter. Frontiers in Plant Science, 2019, 10: 1049. doi: 10.3389/fpls.2019.01049
[15]	WASEEM M, RONG X Y, LI Z G. Dissecting the role of a basic helix-loop-helix transcription factor, SlbHLH22, under salt and drought stresses in transgenic Solanum lycopersicum L.. Frontiers in Plant Science, 2019, 10: 734. doi: 10.3389/fpls.2019.00734
[16]	CHUNTHABUREE S, SAKUANRUNGSIRIKUL S, WONGWARAT T, SANITCHON J, PATTANAGUL W, THEERAKULPISUT T. Changes in anthocyanin content and expression of anthocyanin synthesis genes in seedlings of black glutinous rice in response to salt stress. Asian Journal of Plant Sciences, 2016, 15(3/4): 56-65. doi: 10.3923/ajps.2016.56.65
[17]	AI T N, NAING A H, YUN B W, LIM S H, KIM C K. Overexpression of RsMYB1 enhances anthocyanin accumulation and heavy metal stress tolerance in transgenic Petunia. Frontiers in Plant Science, 2018, 9: 1388. doi: 10.3389/fpls.2018.01388
[18]	邱红梅, 陈亮, 侯云龙, 王新风, 陈健, 马晓萍, 崔正果, 张玲, 胡金海, 王跃强, 邱丽娟. 大豆种子颜色遗传调控机制研究进展. 作物学报, 2021, 47(12): 2299-2313. doi: 10.3724/SP.J.1006.2021.14022
	QIU H M, CHEN L, HOU Y L, WANG X F, CHEN J, MA X P, CUI Z G, ZHANG L, HU J H, WANG Y Q, QIU L J. Research progress on genetic regulatory mechanism of seed color in soybean (Glycine max). Acta Agronomica Sinica, 2021, 47(12): 2299-2313. (in Chinese)
[19]	WANG M, LI W Z, FANG C, XU F, LIU Y C, WANG Z, YANG R, ZHANG M, LIU S L, LU S J, LIN T, TANG J Y, WANG Y Q, WANG H R, LIN H, ZHU B G, CHEN M S, KONG F J, LIU B H, ZENG D L, JACKSON S A, CHU C C, TIAN Z X. Parallel selection on a dormancy gene during domestication of crops from multiple families. Nature Genetics, 2018, 50(10): 1435-1441. doi: 10.1038/s41588-018-0229-2 pmid: 30250128
[20]	CHO Y B, JONES S I, VODKIN L O. Nonallelic homologous recombination events responsible for copy number variation within an RNA silencing locus. Plant Direct, 2019, 3(8): e00162.
[21]	TODD J J, VODKIN L O. Duplications that suppress and deletions that restore expression from a Chalcone synthase multigene family. The Plant Cell, 1996, 8(4): 687-699. doi: 10.2307/3870344
[22]	GUO Y, QIU L J. Allele-specific marker development and selection efficiencies for both flavonoid 3’- hydroxylase and flavonoid 3’,5’-hydroxylase genes in soybean subgenus soja. Theoretical and Applied Genetics, 2013, 126(6): 1445-1455. doi: 10.1007/s00122-013-2063-3
[23]	ZABALA G, VODKIN L. A putative autonomous 20.5 kb-CACTA transposon insertion in an F3'H allele identifies a new CACTA transposon subfamily in Glycine max. BMC Plant Biology, 2008, 8: 124. doi: 10.1186/1471-2229-8-124
[24]	ZABALA G, VODKIN L O. A rearrangement resulting in small tandem repeats in the F3’5’H gene of white flower genotypes is associated with the soybean W1 locus. Crop Science, 2007, 47(S2): s113-s124.
[25]	NITARSKA D, STEFANINI C, HASELMAIR-GOSCH C, MIOSIC S, WALLISER B, MIKULIC-PETKOVSEK M, REGOS I, SLATNAR A, DEBENER T, TEREFE-AYANA D, VILPERTE V, HADERSDORFER J, STICH K, HALBWIRTH H. The rare orange-red colored Euphorbia pulcherrima cultivar ‘Harvest Orange’ shows a nonsense mutation in a flavonoid 3'-hydroxylase allele expressed in the bracts. BMC Plant Biology, 2018, 18(1): 216. doi: 10.1186/s12870-018-1424-0
[26]	VIKHOREV A V, STRYGINA K V, KHLESTKINA E K. Duplicated flavonoid 3’-hydroxylase and flavonoid 3’, 5’- hydroxylase genes in barley genome. PeerJ, 2019, 7: e6266. doi: 10.7717/peerj.6266
[27]	ZABALA G, VODKIN L O. Methylation affects transposition and splicing of a large CACTA transposon from a MYB transcription factor regulating anthocyanin synthase genes in soybean seed coats. PLoS ONE, 2014, 9(11): e111959. doi: 10.1371/journal.pone.0111959
[28]	CHO Y B, JONES S I, VODKIN L O. Mutations in Argonaute5 illuminate epistatic interactions of the K1 and I loci leading to saddle seed color patterns in Glycine max. The Plant Cell, 2017, 29(4): 708-725. doi: 10.1105/tpc.17.00162
[29]	ZOU C, WANG P X, XU Y B. Bulked sample analysis in genetics, genomics and crop improvement. Plant Biotechnology Journal, 2016, 14(10): 1941-1955. doi: 10.1111/pbi.12559 pmid: 26990124
[30]	MICHELMORE R W, PARAN I, KESSELI R V. Identification of markers linked to disease-resistance genes by bulked segregant analysis: A rapid method to detect markers in specific genomic regions by using segregating populations. Proceedings of the National Academy of Sciences of the United States of America, 1991, 88(21): 9828-9832.
[31]	ZHANG G, ANGELES E R, ABENES M L P, KHUSH G S, HUANG N. RAPD and RFLP mapping of the bacterial blight resistance gene xa-13 in rice. Theoretical and Applied Genetics, 1996, 93(1): 65-70. doi: 10.1007/BF00225728
[32]	MA J J, ZHAO Y H, CHEN H, FU C, ZHU L, ZHOU X M, XIA H, HOU L, LI G H, ZHUANG W J, WANG X J, ZHAO C Z. Genome-wide development of polymorphic microsatellite markers and their application in peanut breeding program. Electronic Journal of Biotechnology, 2020, 44: 25-32. doi: 10.1016/j.ejbt.2020.01.004
[33]	PAN J W, ZHOU X M, AHMAD N, ZHANG K, TANG R H, ZHAO H L, JIANG J, TIAN M D, LI C S, LI A Q, ZHANG X Y, HE L Q, MA J, LI X J, TIAN R Z, MA C L, PANDEY M K, VARSHNEY R K, WANG X J, ZHAO C Z. BSA-seq and genetic mapping identified candidate genes for branching habit in peanut. Theoretical and Applied Genetics, 2022, 135(12): 4457-4468. doi: 10.1007/s00122-022-04231-8
[34]	RAMIREZ-GONZALEZ R H, SEGOVIA V, BIRD N, FENWICK P, HOLDGATE S, BERRY S, JACK P, CACCAMO M, UAUY C. RNA-Seq bulked segregant analysis enables the identification of high-resolution genetic markers for breeding in hexaploid wheat. Plant Biotechnology Journal, 2015, 13(5): 613-624. doi: 10.1111/pbi.2015.13.issue-5
[35]	ZEGEYE W A, ZHANG Y X, CAO L Y, CHENG S H. Whole genome resequencing from bulked populations as a rapid QTL and gene identification method in rice. International Journal of Molecular Sciences, 2018, 19(12): 4000. doi: 10.3390/ijms19124000
[36]	HUANG P, JIANG H, ZHU C M, BARRY K, JENKINS J, SANDOR L, SCHMUTZ J, BOX M S, KELLOGG E A, BRUTNELL T P. Sparse panicle1 is required for inflorescence development in Setaria viridis and maize. Nature Plants, 2017, 3: 17054. doi: 10.1038/nplants.2017.54
[37]	ZHAO Y H, MA J J, LI M, DENG L, LI G H, XIA H, ZHAO S Z, HOU L, LI P C, MA C L, YUAN M, REN L, GU J Z, GUO B Z, ZHAO C Z, WANG X J. Whole-genome resequencing-based QTL-seq identified AhTc1 gene encoding a R2R3-MYB transcription factor controlling peanut purple testa colour. Plant Biotechnology Journal, 2020, 18(1): 96-105. doi: 10.1111/pbi.v18.1
[38]	KALENDAR R, BORONNIKOVA S, SEPPÄNEN M. Isolation and purification of DNA from complicated biological samples. Methods in Molecular Biology, 2021, 2222: 57-67. doi: 10.1007/978-1-0716-0997-2_3 pmid: 33301087
[39]	邱丽娟, 常汝镇. 大豆种质资源描述规范和数据标准. 北京: 中国农业出版社, 2006.
	QIU L J, CHANG R Z. Descriptors and Data Standard for Melon (Glycine spp.). Beijing: China Agricuture Press, 2006. (in Chinese)
[40]	LI H, DURBIN R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics, 2009, 25(14): 1754-1760. doi: 10.1093/bioinformatics/btp324 pmid: 19451168
[41]	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 Research, 2010, 20(9): 1297-1303. doi: 10.1101/gr.107524.110 pmid: 20644199
[42]	REUMERS J, DE RIJK P, ZHAO H, LIEKENS A, SMEETS D, CLEARY J, VAN LOO P, VAN DEN BOSSCHE M, CATTHOOR K, SABBE B, DESPIERRE E, VERGOTE I, HILBUSH B, LAMBRECHTS D, DEL-FAVERO J. Optimized filtering reduces the error rate in detecting genomic variants by short-read sequencing. Nature Biotechnology, 2012, 30(1): 61-68. doi: 10.1038/nbt.2053
[43]	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 Lrosophila melanogaster strain w1118; iso-2; iso-3. Fly, 2012, 6(2): 80-92.
[44]	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 Research, 2013, 23(4): 687-697. doi: 10.1101/gr.146936.112 pmid: 23299975
[45]	FEKIH R, TAKAGI H, TAMIRU M, ABE A, NATSUME S, YAEGASHI H, SHARMA S, SHARMA S, KANZAKI H, MATSUMURA H, SAITOH H, MITSUOKA C, UTSUSHI H, UEMURA A, KANZAKI E, KOSUGI S, YOSHIDA K, CANO L, KAMOUN S, TERAUCHI R. MutMap+: Genetic mapping and mutant identification without crossing in rice. PLoS ONE, 2013, 8(7): e68529. doi: 10.1371/journal.pone.0068529
[46]	邓泱泱, 荔建琦, 吴松锋, 朱云平, 陈耀文, 贺福初. nr数据库分析及其本地化. 计算机工程, 2006, 32(5): 71-73, 76.
	DENG Y Y, LI J Q, WU S F, ZHU Y P, CHEN Y W, HE F C. Integrated nr database in protein annotation system and its localization. Computer Engineering, 2006, 32(5): 71-73, 76. (in Chinese)
[47]	ASHBURNER M, BALL C A, BLAKE J A, BOTSTEIN D, BUTLER H, CHERRY J M, DAVIS A P, DOLINSKI K, DWIGHT S S, EPPIG J T, HARRIS M A, HILL D P, ISSEL-TARVER L, KASARSKIS A, LEWIS S, MATESE J C, RICHARDSON J E, RINGWALD M, RUBIN G M, SHERLOCK G. Gene Ontology: Tool for the unification of biology. The gene ontology consortium. Nature Genetics, 2000, 25(1): 25-29. doi: 10.1038/75556 pmid: 10802651
[48]	TATUSOV R L, GALPERIN M Y, NATALE D A, KOONIN E V. The COG database: A tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Research, 2000, 28(1): 33-36.
[49]	KANEHISA M, GOTO S, KAWASHIMA S, OKUNO Y, HATTORI M. The KEGG resource for deciphering the genome. Nucleic Acids Research, 2004, 32 (Supp_1): D277-D280. doi: 10.1093/nar/gkh063
[50]	LU N, RAO X L, LI Y, JUN J H, DIXON R A. Dissecting the transcriptional regulation of proanthocyanidin and anthocyanin biosynthesis in soybean (Glycine max). Plant Biotechnology Jounal, 2021, 19(7): 1429-1442.
[51]	YUAN B Q, YUAN C P, WANG Y M, LIU X D, QI G X, WANG Y N, DONG L C, ZHAO H K, LI Y Q, DONG Y S. Identification of genetic loci conferring seed coat color based on a high-density map in soybean. Frontiers in Plant Science, 2022, 13: 968618. doi: 10.3389/fpls.2022.968618
[52]	AMAROWICZ R, RONALD B P. Legumes as a source of natural antioxidants. European Journal of Lipid Science and Technology, 2008, 110(10): 865-878. doi: 10.1002/ejlt.v110:10
[53]	MALENČIĆ D, CVEJIĆ J, MILADINOVIĆ J. Polyphenol content and antioxidant properties of colored soybean seeds from central Europe. Journal of Medicinal Food, 2012, 15(1): 89-95. doi: 10.1089/jmf.2010.0329 pmid: 21861721
[54]	LINDNER H, RAISSIG M T, SAILER C, SHIMOSATO-ASANO H, BRUGGMANN R, GROSSNIKLAUS U. SNP-Ratio mapping (SRM): Identifying lethal alleles and mutations in complex genetic backgrounds by next-generation sequencing. Genetics, 2012, 191(4): 1381-1386. doi: 10.1534/genetics.112.141341 pmid: 22649081
[55]	ZHAO M M, HU B L, FAN Y W, DING G M, YANG W L, CHEN Y, CHEN Y H, XIE J K, ZHANG F T. Identification, analysis, and confirmation of seed storability-related loci in Dongxiang wild rice (Oryza rufipogon griff.). Genes, 2021, 12(11): 1831. doi: 10.3390/genes12111831
[56]	LIU D, WEI X, SUN D, YANG S, SU H, WANG Z, ZHAO Y, LI L, LIANG J, YANG L, ZHANG X, YUAN Y. An SNP mutation of gene RsPP converts petal color from purple to white in radish (Raphanus sativus L.). Frontiers in Plant Science, 2021, 12: 643579. doi: 10.3389/fpls.2021.643579
[57]	WAMBUGU P, NDJIONDJOP M N, FURTADO A, HENRY R. Sequencing of bulks of segregants allows dissection of genetic control of amylose content in rice. Plant Biotechnology Journal, 2018, 16(1): 100-110. doi: 10.1111/pbi.12752 pmid: 28499072
[58]	LEI L, ZHENG H L, BI Y L, YANG L M, LIU H L, WANG J G, SUN J, ZHAO H W, LI X W, LI J M, LAI Y C, ZOU D T. Identification of a major QTL and candidate gene analysis of salt tolerance at the bud burst stage in rice (Oryza sativa L.) using QTL-seq and RNA-seq. Rice, 2020, 13(1): 55. doi: 10.1186/s12284-020-00416-1
[59]	HOLTON T A, CORNISH E C. Genetics and biochemistry of anthocyanin biosynthesis. The Plant Cell, 1995, 7(7): 1071-1083. doi: 10.1105/tpc.7.7.1071 pmid: 12242398
[60]	WINKEL-SHIRLEY B. Flavonoid biosynthesis. A colorful model for genetics, biochemistry, cell biology, and biotechnology. Plant Physiology, 2001, 126(2): 485-493. doi: 10.1104/pp.126.2.485
[61]	JAAKOLA L. New insights into the regulation of anthocyanin biosynthesis in fruits. Trends in Plant Science, 2013, 18(9): 477-483. doi: 10.1016/j.tplants.2013.06.003 pmid: 23870661
[62]	XU W J, DUBOS C, LEPINIEC L. Transcriptional control of flavonoid biosynthesis by MYB-bHLH-WDR complexes. Trends in Plant Science, 2015, 20(3): 176-185. doi: 10.1016/j.tplants.2014.12.001 pmid: 25577424
[63]	LI Y Q, SHAN X T, TONG L N, WEI C, LU K Y, LI S Y, KIMANI S, WANG S C, WANG L, GAO X. The conserved and particular roles of the R2R3-MYB regulator FhPAP1 from Freesia hybrida in flower anthocyanin biosynthesis. Plant and Cell Physiology, 2020, 61(7): 1365-1380. doi: 10.1093/pcp/pcaa065
[64]	高瑞芳. GmMYBA2与GmMYBR协同调控大豆种皮颜色的机制解析[D]. 长春: 东北师范大学, 2021.
	GAO R F. Mechanism analysis of GmMYBA2 and GmMYBR synergistic regulation of soybean seed coat color[D]. Changchun: Northeast Normal University, 2021. (in Chinese)
[65]	ZHANG Z Y, SHI Y N, MA Y C, YANG X F, YIN X R, ZHANG Y Y, XIAO Y W, LIU W L, LI Y D, LI S J, LIU X F, GRIERSON D, ALLAN A C, JIANG G H, CHEN K S. The strawberry transcription factor FaRAV1 positively regulates anthocyanin accumulation by activation of FaMYB10 and anthocyanin pathway genes. Plant Biotechnology Journal, 2020, 18(11): 2267-2279. doi: 10.1111/pbi.v18.11
[66]	XU Z S, YANG Q Q, FENG K, YU X, XIONG A S. DcMYB113, a root-specific R2R3-MYB, conditions anthocyanin biosynthesis and modification in carrot. Plant Biotechnology Journal, 2020, 18(7): 1585-1597. doi: 10.1111/pbi.v18.7
[67]	TIAN J, PENG Z, ZHANG J, SONG T T, WAN H H, ZHANG M L, YAO Y C. McMYB10 regulates coloration via activating McF3'H and later structural genes in ever-red leaf crabapple. Plant Biotechnology Journal, 2015, 13(7): 948-961. doi: 10.1111/pbi.2015.13.issue-7
[68]	SHIMADA S, OTSUKI H, SAKUTA M. Transcriptional control of anthocyanin biosynthetic genes in the Caryophyllales. Journal of Experimental Botany, 2007, 58(5): 957-967. pmid: 17185736
[69]	YAN F, DI S, TAKAHASHI R. CACTA-superfamily transposable element is inserted in MYB transcription factor gene of soybean line producing variegated seeds. Genome, 2015, 58(8): 365-374. doi: 10.1139/gen-2015-0054 pmid: 26360633
[70]	KOVINICH N, SALEEM A, ARNASON J T, MIKI B. Identification of two anthocyanidin reductase genes and three red-brown soybean accessions with reduced anthocyanidin reductase-1 mRNA, activity, and seed coat proanthocyanidin amounts. Journal of Agricultural and Food Chemistry, 2012, 60(2): 574-584. doi: 10.1021/jf2033939

Metrics

Viewed

Full text

Abstract

Cited

Shared

Discussed

Comments

Recommended 0

No Suggested Reading articles found!

样品 Sample	清洁read对数 Clean reads	质量值>30碱基 Q30 (%)	可定位清洁read Mapped (%)	平均覆盖深度 Ave depth	至少覆盖1次的碱基 Cov≥1× (%)
SN	73658060	92.50	99.03	16	97.94
TX	74839493	93.45	99.19	19	97.75
Y	110060520	94.05	99.25	29	99.03
R	109932563	93.05	99.41	30	99.03

关联分析类型 Type of correlation analysis	候选区域位置 Location of candidate areas (bp)	区域长度 Size of area (Mb)	基因总数 Gene number
SNP-ED	Chr.08: 3500000-12530000	9.03	1174
SNP-index	Chr.06: 32790000-32800000	0.01	1
	Chr.06: 32940000-33020000	0.08	2
	Chr.08: 3530000-12280000	8.75	1138
SNP分析结果的交集 Intersection of the results of SNP analyses	Chr.08: 3530000-12280000	8.75	1138
InDel-ED	Chr.08: 3290000-12530000	9.24	1201
InDel-index	Chr.08: 3510000-12190000	8.68	1132
InDel分析结果的交集 Intersection of the results of InDel analyses	Chr.08: 3510000-12190000	8.68	1132
所有关联分析结果的交集 Intersection of all correlation analysis results	Chr.08: 3530000-12190000	8.66	1127

Pigment Identification and Gene Mapping in Red Seed Coat of Soybean

RichHTML

PDF

Abstract

Cite this article

share this article

Figures/Tables 10

References 70

Related Articles 15

Metrics

Comments

Recommended 0

[1]	LI YongJuan, ZHANG YueTong, WANG YiBo, ZHAO ChangJiang, SONG Jie, CHEN XueLi, YAO Qin. Effects of Biochar Application on the Abundance and Community Composition of Nitrogen-Fixing Microbial nifH Gene in Soybean Rotation and Continuous Cropping Systems [J]. Scientia Agricultura Sinica, 2026, 59(6): 1272-1285.
[2]	LIU FangDong, SUN Lei, WANG WuBin, ZHAO JinMing, GAI JunYi. Changes of Cropping System and Suggestions on Ecological Cultivation Regions of Soybeans in China [J]. Scientia Agricultura Sinica, 2026, 59(3): 486-498.
[3]	PEI HongXia, WANG LuYao, JIANG YaPing, LI ShengMei, GAO JingXia. Identification of Nuclear Male Sterility Genes in Pepper Based on BSA-Seq and Proteomics [J]. Scientia Agricultura Sinica, 2026, 59(3): 637-654.
[4]	CAI TingYang, ZHU YuPeng, LI RuiDong, WU ZongSheng, XU YiFan, SONG WenWen, XU CaiLong, WU CunXiang. Effects of Leaf-Cutting at Seedling Stage on Photosynthetic Characteristics, Pod Distribution and Yield Formation in Soybean in the Huang-Huai-Hai Region [J]. Scientia Agricultura Sinica, 2026, 59(2): 292-304.
[5]	WU Qiong, XIE XiangTing, WANG Lei, MOU Yong, LI JinWei. Development and Validation of Event-Specific PCR Method for the Quantification of Genetically Modified Soybean DBN8205 [J]. Scientia Agricultura Sinica, 2026, 59(1): 29-40.
[6]	TANG Yu, LEI BiXin, WANG ChuanWei, YAN XuanTao, WANG Hao, ZHENG Jie, ZHANG WenJing, MA ShangYu, HUANG ZhengLai, FAN YongHui. Response Mechanism of Anthocyanin Accumulation in Colored Wheat to Post-Anthesis High Temperature Stress [J]. Scientia Agricultura Sinica, 2025, 58(6): 1083-1101.
[7]	LIU LuPing, HU XueJie, QI Jin, CHEN Qiang, LIU Zhi, ZHAO TianTian, SHI XiaoLei, LIU BingQiang, MENG QingMin, ZHANG MengChen, HAN TianFu, YANG ChunYan. Cloning of the Promoters and Analysis of Expression Patterns of Maturity Genes E1 and E2 in Soybean [J]. Scientia Agricultura Sinica, 2025, 58(5): 840-850.
[8]	XIAO ChangChun, WEI XinYu, ZENG YueHui, HUANG JianHong, XU XuMing. Accumulation Characteristics of Anthocyanins in Black Rice Under Different Sowing Dates and Its Relationship with Meteorological Factors [J]. Scientia Agricultura Sinica, 2025, 58(5): 890-906.
[9]	ZHENG Yu, CHEN Yi, TI JinSong, SHI LongFei, XU XiaoBo, LI YuLin, GUO Rui. Evaluation of Carbon Footprint and Economic Benefit of Different Tobacco Rotation Patterns [J]. Scientia Agricultura Sinica, 2025, 58(4): 733-747.
[10]	GUO AoLin, LIN JunXuan, LAI GongTi, HE LiYuan, CHE JianMei, PAN Ruo, YANG FangXue, HUANG YuJi, CHEN GuiXin, LAI ChengChun. Effect of VdF3′5′H2 Overexpression on the Accumulation of Anthocyanin Composition in Spine Grape Cells [J]. Scientia Agricultura Sinica, 2025, 58(4): 802-818.
[11]	ZHUANG LiHua, LUO Lei, ZHAO ChunFang, WANG JiZhong, ZHANG YaDong, HE Lei. Identification and Gene Mapping of Rice Grain Shape Mutant sgd13 [J]. Scientia Agricultura Sinica, 2025, 58(24): 5097-5109.
[12]	ZHANG Qi, XUE FuZhen, YANG XiuJie, JIANG SuYang, HUANG XueJuan, MA JiaYi, ZHANG ZheWen, XU JieFei. Study on the Function of Soybean Nicotinamide Enzyme GmNIC1 Gene Under Saline Alkali Stress [J]. Scientia Agricultura Sinica, 2025, 58(24): 5128-5142.
[13]	MA HeXiao, GE GuoLong, ZHANG XiangQian, LU ZhanYuan, WANG ManXiu, RONG MeiRen, SHI JingJing, ZHANG DeJian, SUN XuePing. Effects of Different Crop Rotation Systems on Soil Readily Oxidized Organic Carbon and Carbon Pool Activity Differences [J]. Scientia Agricultura Sinica, 2025, 58(24): 5201-5215.
[14]	GAO ChunHua, ZHAO HaiJun, ZHAO FengTao, KONG WeiLin, JU FeiYan, LI ZongXin, SHI DeYang, LIU Ping. Effect of Growth Regulators on the Stem Characteristics and Yield of Summer Maize in Maize-Soybean Strip Intercropping [J]. Scientia Agricultura Sinica, 2025, 58(23): 4920-4935.
[15]	YANG ShuQi, ZHAO YingXing, QIAN Xin, ZHANG XuePeng, MENG WeiWei, SUI Peng, LI ZongXin, CHEN YuanQuan. Comprehensive Evaluation of the Maize-Soybean Intercropping Pattern in the Huang-Huai Region [J]. Scientia Agricultura Sinica, 2025, 58(23): 4936-4951.