大豆B类花器官特征基因的生物信息学分析

王曦昕; 蒋炳军; 袁珊; 武婷婷; 孙石; 张亮生; 韩天富

大豆B类花器官特征基因的生物信息学分析

王曦昕^1,2,
蒋炳军^2,,
袁珊²,
武婷婷²,
孙石²,
张亮生³,
韩天富^1,2,

1. 东北农业大学农学院;
2. 中国农业科学院作物科学研究所;
3. 浙江大学农业与生物技术学院

基金项目:

国家重点研发计划(2023YFD1201300)

现代农业产业技术体系建设专项(CARS-04)

详细信息

作者简介:
王曦昕(1997—),女,硕士研究生,主要从事大豆分子育种研究。E-mail:wangxixin717ww@163.com

通讯作者:
蒋炳军(1977—),男,博士,副研究员,主要从事大豆分子育种研究。E-mail:jiangbingjun@caas.cn

韩天富(1963—),男,博士,研究员,主要从事大豆遗传育种研究。E-mail:hantianfu@caas.cn

中图分类号: S565.1
计量
- 文章访问数: 14
- HTML全文浏览量: 2
- PDF下载量: 3
出版历程
- 收稿日期: 2023-09-27
- 刊出日期: 2024-03-19

Bioinformatics Analysis of B-class Floral Organ Identity Genes in Soybean

1. College of Agriculture, Northeast Agricultural University;
2. Institute of Crop Sciences, Chinese Academy of Agricultural Sciences;
3. College of Agriculture and Biotechnology, Zhejiang University

摘要

摘要: 大豆花器官较小且闭花授粉，导致人工杂交效率低，品种遗传基础狭窄。MADS-box基因家族成员APETALA3(AP3)和PISTILLATA(PI)作为花发育ABCDE模型中的B类基因，共同控制花瓣与雄蕊的形成，在花器官形态建成中发挥重要作用。为明确大豆中B类基因的进化模式，并探究其在不同大豆品种中的遗传变异，本研究通过生物信息学手段对大豆B类基因进行了基因结构、系统进化、保守基序、共线性、单倍型分析及物理性质预测等研究。结果显示：大豆基因组中11个B类基因，分别属于3个亚组，其中GmAP304(Glyma.04G027200)、GmAP306(Glyma.06G027200)、GmAP303(Glyma.03G111500)、GmAP316(Glyma.16G105600)和GmAP312(Glyma.12G118100)属于paleoAP3亚组，GmTM601(Glyma.01G169600)和GmTM611(Glyma.11G073700)属于TM6亚组，GmPI13(Glyma.13G034100)、GmPI14(Glyma.14G155100)、GmPI04(Glyma.04G245500)和GmPI06(Glyma.06G117600)属于PI亚组，且各亚组B类基因结构相对保守；大豆B类基因编码的蛋白中共有10个motif,其中motif 1、motif 4和motif 5与MADS结构域重叠。表达量数据分析显示，GmAP304、GmAP306、GmPI04、GmPI06、GmPI13、GmPI14、GmTM601和GmTM611在大豆花中有较高表达。结合单倍型分析发现，GmAP304、GmAP312、GmPI06、GmPI13和GmPI14在栽培大豆中只包含1种单倍型，比其它大豆B类基因更加保守，可能在控制花器官形成中行使更为重要的功能。本研究结果有助于完善大豆花器官发育模型，进一步阐明B类基因的功能，为大豆花器官的改造提供分子靶点，对提高大豆育种效率、拓宽品种遗传基础具有重要意义。
- 大豆 /
- APETALA3 /
- PISTILLATA /
- MADS-box /
- 花器官特征基因
Abstract: Soybean has small-sized flowers and the property of self-pollination, leading to low efficiency of artificial hybridization and narrow genetic basis of varieties. APETALA3（AP3） and PISTILLATA（PI）, belonging to MADS-box gene family and class B genes in the floral ABCDE model, jointly control the formation of flower petals and stamens and play important roles in floral organ morphogenesis. In order to identify the evolutionary pattern of B-class genes and explore the genetic diversity among soybean varieties, we analyzed gene structure, phylogenetic tree, conservative motif, collinearity, haplotypes of B-class genes in soybean by bioinformatics methods. It was shown that there are 11 B-class genes in soybean genome. Of them, GmAP304（Glyma.04G027200）, GmAP306（Glyma.06G027200）, GmAP303（Glyma.03G111500）, GmAP316（Glyma.16G105600） and GmAP312（Glyma.12G118100） belong to the paleoAP3 subgroup, GmTM601（Glyma.01G169600） and GmTM611（Glyma.11G073700） belong to the TM6 subgroup, and GmPI13（Glyma.13G034100）, GmPI14（Glyma.14G155100）, GmPI04（Glyma.04G245500） and GmPI06（Glyma.06G117600） belong to the PI subgroup. The gene structures of B-class genes in each subgroup are relatively conservative. Ten motifs are found in the proteins encoded by B-class genes in soybean, among which motif 1, motif 4, and motif 5 overlap with the MADS domain. Transcriptome data indicated that GmAP304, GmAP306, GmPI04, GmPI06, GmPI13, GmPI14, GmTM601 and GmTM611 are highly expressed in flowers of soybean. Moreover, haplotype analysis showed that five B-class genes including GmAP304, GmAP312, GmPI06, GmPI13 and GmPI14 each contain only one haplotype in cultivated soybean, indicating that they are more conservative than other B-class genes, and may play more important roles in controlling floral organ formation. These results are helpful for improving the developmental model of flower organs in soybean and further elucidating the functions of B-class genes, which will facilitate the identification of molecular targets for the modification of flower organs, and will be of great significance for improving soybean breeding efficiency and broadening the genetic basis of new varieties.
- soybean /
- APETALA3 /
- PISTILLATA /
- MADS-box /
- floral organ identity genes

HTML全文

参考文献(40)

[1]	YOSHIMURA Y.Wind tunnel and field assessment of pollen dispersal in soybean[Glycine max (L.) Merr][J].Journal of Plant Research,2011,124(1):109-114.
[2]	闫昊,张井勇,彭宝,等.大豆异交率性状研究概述[J].安徽农业科学,2017,45(36):14-16.(YAN H,ZHANG J Y,PENG B,et al.Overview of outcrossing rate traits in soybeans[J].Journal of Anhui Agricultural Sciences,2017,45(36):14-16.)
[3]	BEARD B H,KNOWLES P F.Frequency of cross-pollination of soybeans after seed Irradiation[J].Crop Science,1971,11(4):489-492.
[4]	JARNE P,DAVID P.Quantifying inbreeding in natural populations of hermaphroditic organisms[J].Heredity,2008,100(4):431-439.
[5]	WEBER C R,HANSON W D.Natural hybridization with and wit-hout ionizing radiation in soybeans[J].Crop Science,1961,1(6):389-392.
[6]	李继存,黄新阳,王妙,等.大豆杂交中伪杂种产生的原因分析[J].大豆科学,2012,31(3):492-494.(LI J C,HUANG X Y,WANG M,et al.Analysis on reasons for false hybrid seeds of soybean[J].Soybean Science,2012,31(3):492-494.)
[7]	曹永强,宋书宏,王文斌,等.拓宽大豆育种遗传基础研究进展[J].辽宁农业科学,2005(6):34-36.(CAO Y Q,SONG S H,WANG W B,et al.Research advance on broadening genetic base of soybean breeding[J].Liaoning Agricultural Sciences,2005(6):34-36.)
[8]	HUANG W,HOU J,HU Q,et al.Pedigree-based genetic dissection of quantitative loci for seed quality and yield characters in improved soybean[J].Molecular Breeding,2021,41(2):14.
[9]	谢甫绨.大豆雄性不育及杂种优势利用研究进展[J].沈阳农业大学学报,2008,39(2):131-136.(XIE F T.Review of soybean male sterility and heterosis utilization[J].Journal of Shenyang Agricultural University,2008,39(2):131-136.)
[10]	KAY S.The molecular and genetic control of ovule development[J].Current Opinion in Plant Biology,1999,2(1):13-17.
[11]	ANGENENT G C,FRANKEN J,BUSSCHER M,et al.A novel class of MADS box genes is involved in ovule development in petunia[J].The Plant Cell,1995,7(10):1569-1582.
[12]	FANG Z W,QI R,LI X F,et al.Ectopic expression of FaesAP3,a Fagopyrum esculentum (Polygonaceae) AP3 orthologous gene rescues stamen development in an Arabidopsis ap3 mutant[J].Gene,2014,550(2):200-206.
[13]	THEIBEN G,MELZER R,RÜMPLER F.MADS-domain transc-ription factors and the floral quartet model of flower development:Linking plant development and evolution[J].Development,2016,143(18):3259-3271.
[14]	丛楠,程治军,万建民.控制花器官发育的ABCDE模型[J].中国农学通报,2007,23(7):124-128.(CONG N,CHENG Z J,WAN J M.The ABCDE model of floral organ development[J].Chinese Agricultural Science Bulletin,2007,23(7):124-128.)
[15]	黄方,迟英俊,喻德跃.植物MADS-box基因研究进展[J].南京农业大学学报,2012,35(5):9-18.(HUANG F,CHI Y J,YU D Y.Research advances of MADS-box genes in plants[J].Journal of Nanjing Agricultural University,2012,35(5):9-18.)
[16]	HIBINO Y,KITAHARA K,HIRAI S,et al.Structural and functional analysis of rose class B MADS-box genes ‘MASAKO BP,euB3,and B3’:Paleo-type AP3 homologue ‘MASAKO B3’ association with petal development[J].Plant Science,2006,170(4):778-785.
[17]	KRAMER E M,DORIT R L,IRISH V F.Molecular evolution of genes controlling petal and stamen development:Duplication and divergence within the APETALA3 and PISTILLATA MADS-box gene lineages[J].Genetics,1998,149(2):765-783.
[18]	LIU Y,NAKAYAMA N,SCHIFF M,et al.Virus induced gene silencing of a DEFICIENS ortholog in Nicotiana benthamiana[J].Plant Molecular Biology,2004,54(5):701-711.
[19]	VANDENBUSSCHE M,ZETHOF J,ROYAERT S,et al.The duplicated B-class heterodimer model:Whorl-specific effects and complex genetic interactions in Petunia hybrida flower development[J].The Plant Cell,2004,16(3):741-754.
[20]	ROQUE E,SERWATOWSKA J,CRUZ ROCHINA M,et al.Functional specialization of duplicated AP3-like genes in Medicago truncatula[J].The Plant Journal:for Cell and Molecular Biology,2013,73(4):663-675.
[21]	SEVERIN A J,CANNON S B,GRAHAM M M,et al.Changes in twelve homoeologous genomic regions in soybean following three rounds of polyploidy[J].The Plant Cell,2011,23(9):3129-3136.
[22]	SCHMUTZ J,CANNON S B,SCHLUETER J,et al.Genome sequence of the palaeopolyploid soybean[J].Nature,2010,463:178-183.
[23]	ROULIN A,AUER P L,LIBAULT M,et al.The fate of dupli-cated genes in a polyploid plant genome[J].The Plant Journal:for Cell and Molecular Biology,2013,73(1):143-153.
[24]	胡瑞波,范成明,李宏宇,等.大豆MIKC型MADS-box基因家族分析[J].分子植物育种,2009,7(3):429-436.(HU R B,FAN C M,LI H Y,et al.Analysis of MIKC-type MADS-box genes in soybean (Glycine max)[J].Molecular Plant Breeding,2009,7(3):429-436.)
[25]	SHEN G,JIA Y,WANG W L.Evolutionary divergence of motifs in B-class MADS-box proteins of seed plants[J].Journal of Biological Research,2021,28(1):12.
[26]	ZHANG A,HE H,LI Y,et al.MADS-box subfamily gene GmAP3 from Glycine max regulates early flowering and flower development[J].International Journal of Molecular Sciences,2023,24(3):2751.
[27]	MA W Y,LIU W,HOU W S,et al.GmNMH7,a MADS-box transcription factor,inhibits root development and nodulation of soybean (Glycine max[L.]Merr.)[J].Journal of Integrative Agriculture,2019,18(3):553-562.
[28]	LAM H M,XU X,LIU X,et al.Resequencing of 31 wild and cultivated soybean genomes identifies patterns of genetic diversity and selection[J].Nature Genetics,2010,42(12):1053-1059.
[29]	ZHOU Z,JIANG Y,WANG Z,et al.Resequencing 302 wild and cultivated accessions identifies genes related to domestication and improvement in soybean[J].Nature Biotechnology,2015,33:408-414.
[30]	QI X,JIANG B,WU T,et al.Genomic dissection of widely planted soybean cultivars leads to a new breeding strategy of crops in the post-genomic era[J].The Crop Journal,2021,9(5):1079-1087.
[31]	ZHANG T,WU T,WANG L,et al.A combined linkage and GWAS analysis identifies QTLs linked to soybean seed protein and oil content[J].International Journal of Molecular Sciences,2019,20(23):5915.
[32]	YUE Y,SUN S,LI J,et al.GmFULa improves soybean yield by enhancing carbon assimilation without altering flowering time or maturity[J].Plant Cell Reports,2021,40(10):1875-1888.
[33]	JIANG B,ZHANG S,SONG W,et al.Natural variations of FT family genes in soybean varieties covering a wide range of maturity groups[J].BMC Genomics,2019,20(1):230.
[34]	DUARTE J M,CUI L,WALL P K,et al.Expression pattern shifts following duplication indicative of subfunctionalization and neofunctionalization in regulatory genes of Arabidopsis[J].Molecular Biology and Evolution,2006,23(2):469-478.
[35]	MOORE R C,PURUGGANAN M D.The evolutionary dynamics of plant duplicate genes[J].Current Opinion in Plant Biology,2005,8(2):122-128.
[36]	KIM S,YOO M J,ALBERT V A,et al.Phylogeny and diversi-fication of B-function MADS-box genes in angiosperms:Evolutionary and functional implications of a 260-million-year-old duplication[J].American Journal of Botany,2004,91(12):2102-2118.
[37]	VANDENBUSSCHE M,THEISSEN G,VAN DE PEER Y,et al.Structural diversification and neo-functionalization during floral MADS-box gene evolution by C-terminal frameshift mutations[J].Nucleic Acids Research,2003,31(15):4401-4409.
[38]	黄和喜,王岩,许玉超,等.不结球白菜雄蕊瓣化相关 AP3 基因的克隆和表达分析[J].南京农业大学学报,2015,38(5):748-756.(HUANG H X,WANG Y,XU Y C,et al.Clone and expression analysis of stamen patelody-associated AP3 genes from non-heading Chinese cabbage[J].Journal of Nanjing Agricultural University,2015,38(5):748-756.)
[39]	YAO S G,OHMORI S,KIMIZU M,et al.Unequal genetic redundancy of rice PISTILLATA orthologs,OsMADS2 and OsMADS4,in lodicule and stamen development[J].Plant and Cell Physiology,2008,49(5):853-857.
[40]	WANG H,ZHANG L,CAI Q,et al.OsMADS32 interacts with PI-like proteins and regulates rice flower development[J].Journal of Integrative Plant Biology,2015,57(5):504-513.