小麦TaDRO与根系形态的关联分析及在中国和全球 品种中的地理分布与演变

doi:10.3864/j.issn.0578-1752.2018.10.001

摘要/Abstract

摘要：

目的根系改良是提高小麦抗逆性和产量的关键因素之一。通过克隆不同根系类型小麦品种的根系相关基因TaDRO,分析其与小麦重要农艺性状的关系,开发标记,为品种改良提供理论依据和技术支撑。方法以根系性状多态性较高的21份普通小麦为材料,测序分析TaDRO-5A、TaDRO-5B和TaDRO-5D的序列多态性;利用“中国春”-缺体四体材料对其进行染色体定位,并用最新版的中国春基因组序列对其进行精细物理定位,根据TaDRO-5A和TaDRO-5B序列多态性开发分子标记;以323份普通小麦构成的自然群体为材料进行TaDRO单元型与表型性状的关联分析。结果克隆了小麦TaDRO的A、B、D基因组序列,利用最新版的中国春基因组序列分别将TaDRO-5A、TaDRO-5B和TaDRO-5D定位于小麦染色体5A、5B和5D上,分别位于426.15、381.00和327.60 Mb处;在TaDRO-5A全长序列中共检测到3个SNP,形成Hap-5A-A和Hap-5A-C 2种单元型,根据启动子区-2 271 bp的序列差异,开发出分子标记TaDRO-5A-KASP。在TaDRO-5B全长序列中共检测到17个SNP和1个InDel,形成Hap-5B-Ⅰ和Hap-5B-Ⅱ 2种单元型,根据-300 bp的InDel开发了分子标记TaDRO-5B-InDel。关联分析表明,TaDRO-5A与株高、千粒重和根系生长角度显著相关,Hap-5A-A是增大根系生长角度、降低株高、增加千粒重的浅根型单元型,而Hap-5A-C是减小根系生长角度、增加株高、降低千粒重的深根型单元型。TaDRO-5B与株高显著相关,Hap-5B-Ⅰ是增加株高和降低千粒重的深根型单元型,Hap-5B-Ⅱ是降低株高和增加千粒重的浅根型单元型。在地方品种中,Hap-5A-C和Hap-5B-Ⅰ为优势单元型,在育成品种中,Hap-5A-A和Hap-5B-Ⅱ为优势单元型;深根型单元型Hap-5A-C和Hap-5B-Ⅰ在干旱、半干旱麦区品种中的分布频率高于湿润麦区;在全球地理分布中,干旱麦区品种中Hap-5A-C为优势单元型,但Hap-5B-I优势不明显。随着育种年代推进,小麦品种中浅根型单元型Hap-5A-A和Hap-5B-Ⅱ的频率增加。结论小麦根系相关基因TaDRO的Hap-5A-C和Hap-5B-Ⅰ是增加株高和降低千粒重的深根型单元型,Hap-5A-A和Hap-5B-Ⅱ是降低株高和增加千粒重的浅根型单元型;随着灌溉和化肥用量的增加,中国小麦品种逐步由深根、高秆类型转变为浅根、矮秆类型;利用分子标记选择矮秆、深根类型,可能提高品种水肥利用效率。

关键词: 小麦, 根系形态, TaDRO, 单元型, 关联分析

Abstract:

【Objective】 Root improvement is one of the key factors to improve stress resistance and yield of wheat. Root architecture related genes, homoeologous TaDRO, are cloned from cultivars with different root phenotypes. Molecular markers are developed to detect its relationship with important agronomic traits of wheat. which could provide technical support for wheat improvement. 【Method】 Polymorphic sites of TaDRO-A, -B and -D were detected in 21 common wheat accessions with high diversity. Physical locations of three homoeologues were determined based on the newest genome sequence of Chinese Spring. Molecular markers were developed according to the polymorphic sites at TaDRO-5A and -5B. Association analysis between genotypes and phenotypic traits were carried out in a natural population of 323 accessions. 【Result】 The three homoeologous genes of TaDRO-A, -B and -D were cloned. TaDRO-A, -B and -D were located on chromosomes 5A (426.15 Mb), 5B (381.00 Mb) and 5D (327.60 Mb), respectively. Three SNPs were detected at TaDRO-A among 21 accessions and two haplotypes were formed, Hap-5A-A and Hap-5A-C. A molecular marker, TaDRO-5A-KASP, was developed based on the SNP located at position of -2271 bp in the promoter region. Thirteen SNPs and one InDel in the promoter region, four SNPs in the coding region were detected at TaDRO-5B, formed two haplotypes, Hap-5B-Ⅰ and Hap-5B-Ⅱ. The marker TaDRO-5B-InDel was developed based on the Indel at position of -300 bp. Association analysis showed that haplotypes of TaDRO-5A were significantly correlated with plant height (PH), thousand kernel weight (TKW) and root growth angle (RGA). The genetic effects on Hap-5A-A showed RGA and TKW increasing, and root depth and PH decreasing, while those on Hap-5A-C exhibited the opposite effect. The effects of Hap-5B-Ⅰ exhibited root depth and PH increasing, and TKW decreasing, while those of Hap-5B-Ⅱ were the opposite. Hap-5A-C and Hap-5B-Ⅰ were favored haplotypes in landraces while they were non-favored ones in modern cultivars. The frequencies of Hap-5A-C and Hap-5B-Ⅰ in arid and semi-arid areas were higher than those in wet areas in China. Hap-5A-C was favored haplotype in dry regions worldwide. Frequencies of Hap-5A-A and Hap-5B-Ⅱ were increasing in breeding process, respectively.【Conclusion】 Hap-5A-C and Hap-5B-Ⅰ are associated with deeper root, higher PH and lower TKW, whereas Hap-5A-A and Hap-5B-Ⅱ behave the opposite. Wheat cultivars showed root depth and plant height decreasing in breeding process due to development of irrigation system and nitrogen industries. The developed molecular markers might be used to select the ideotypes of cultivars for higher efficiency use of water and nitrogen.

Key words: wheat, root architecture, TaDRO, haplotype, association analysis

张维军, 李甜, 秦琳, 赵静, 赵俊杰, 柳洪, 侯健, 郝晨阳, 陈东升, 魏亦勤, 景蕊莲, 张学勇. 小麦TaDRO与根系形态的关联分析及在中国和全球品种中的地理分布与演变[J]. 中国农业科学, 2018, 51(10): 1815-1829.

WeiJun ZHANG, Tian LI, Lin QIN, Jing ZHAO, JunJie ZHAO, Hong LIU, Jian HOU, ChenYang HAO, DongSheng CHEN, YiQin WEI, RuiLian JIN, XueYong ZHANG. TaDRO, A Gene Associated with Wheat Root Architectures, Its Global Distribution and Evolution in Breeding[J]. Scientia Agricultura Sinica, 2018, 51(10): 1815-1829.

0
/ / 推荐

导出引用管理器 EndNote|Reference Manager|ProCite|BibTeX|RefWorks

链接本文: https://www.chinaagrisci.com/CN/10.3864/j.issn.0578-1752.2018.10.001

https://www.chinaagrisci.com/CN/Y2018/V51/I10/1815

图/表 9

图1

图2

图3

表1

表2

图4

图5

图6

图7

参考文献 53

[1]	杨方人. 旱作大豆高产综合技术对根系发育及生理功能影响的研究. 大豆科学, 1987, 6(3): 225-230.
	YANG F R.The effect of the high-yield comprehensive agrotechniques of dry-farming on development of soybean roots.Soybean Science, 1987, 6(3): 225-230. (in Chinese)
[2]	王法宏, 任德昌, 王旭清, 曹宏鑫, 余松烈, 于振文. 施肥对小麦根系活性、延缓旗叶衰老及产量的效应. 麦类作物学报, 2001, 27(3): 51-54. doi: 10.7606/j.issn.1009-1041.2001.03.068
	WANG F H, REN D C, WANG X Q, CAO H X, YU S L, YU Z W.Effect of applying fertilizer on root activity, delaying the senescence of the flag leaf and yield in winter wheat.Journal of Triticeae Crops, 2001, 27(3): 51-54. (in Chinese) doi: 10.7606/j.issn.1009-1041.2001.03.068
[3]	李鲁华, 陈树宾, 秦莉, 孔祥丽, 李世清. 不同土壤水分条件下春小麦品种根系功能效率的研究. 中国农业科学, 2002, 35(7): 867-871.
	LI L H, CHEN S B, QIN L, KONG X L, LI S Q.Study on root function efficiency of spring wheats under different moisture condition.Scientia Agricultura Sinica, 2002, 35(7): 867-871. (in Chinese)
[4]	PENG Y C, MA W Y, CHEN L L, YANG L, LI S J, ZHAO H T, ZHAO Y K, JIN W H, LI N, BEVAN M W, LI X, TONG Y P, LI Y H.Control of root meristem size by DA1-RELATED PROTEIN2 in Arabidopsis. Plant Physiology, 2013, 161(3): 1542-1556.
[5]	YUSAKU U, KAZUHIKO S, SATOSHI O, JAGADISHI R, MANABU I, NAHO H, YUKA K, YOSHIAKI I, KAZUKO O, NORIKO K, HARUHIKO I, HINAKO T, RITSUKO M, YOSHIAKI N, WU J Z, TAKASHI M, TOSHIYUKI T, KAZUTOSHI O, MASAHIRO Y.Control of root system architecture by DEEPER ROOTING 1 increases rice yield under drought conditions. Nature Genetics, 2013, 45(9): 1097-1102. doi: 10.1038/ng.2725 pmid: 23913002
[6]	SHARMA S, XU S, EHDAIE B, HOOPS A, TIMOTHY J, ADAM J, LUKASZEWSKI J, WAINES G.Dissection of QTL effects for root traits using a chromosome arm-specific mapping population in bread wheat.Theoretical and Applied Genetics, 2011, 122: 759-769.
[7]	JIA Y B, YANG X E, FENG Y, JILANI G.Differential response of root morphology to potassium deficient stress among rice genotypes varying in potassium efficiency.Journal of Zhejiang University: Science B, 2008, 9: 427-434. doi: 10.1631/jzus.B0710636 pmid: 18500783
[8]	BAI C H, LIANG Y L, HAWKESFORD M J.Identification of QTLs associated with seedling root traits and their correlation with plant height in wheat.Journal of Experimental Botany, 2013, 64: 1745-1753. doi: 10.1093/jxb/ert041 pmid: 23564959
[9]	LOPES M S, REYNOLDS M P.Partioning of assimilates to deeper roots is associated with cooler canopies and increased yield under drought in wheat.Functional Plant Biology, 2010, 37(2): 147-156.
[10]	HOCHHOLDINGER F.The maize root system: Morphology, anatomy and genetics//BENNETZEN J, HAKE S. The Handbook of Maize. New York: Springer, 2009: 145-160.
[11]	COUNDERT Y, PERIN C, COURTOIS B, KHONG N G, GANTET P.Genetic control of root development in rice, the model cereal.Trends in Plant Science, 2010, 15: 219-226. doi: 10.1016/j.tplants.2010.01.008 pmid: 20153971
[12]	CAO P, REN Y Z, ZHANG K P, TENG W, ZHAO X Q, DONG Z Y, LIU Y, QIN H J, LI Z S, WANG D W, TONG Y P.Further genetic analysis of a major quantitative trait locus controlling root length and related traits in common wheat.Molecular Breeding, 2014, 33(4): 975-985. doi: 10.1007/s11032-013-0013-z
[13]	GUPTA P K, RUSTGI S, KULWAL P L.Linkage disequilibrium and association studies in higher plants: Present status and future prospects.Plant Molecular Biology, 2005, 57(4): 461-485. doi: 10.1007/s11103-005-0257-z pmid: 15821975
[14]	WANG L F, GE H M, HAO C Y, DONG Y C, ZHANG X Y.Identifying loci influencing 1,000-kernel weight in wheat by microsatellite screening for evidence of selection during breeding. PLoS ONE, 2012, 7(2): e29432. doi: 10.1371/journal.pone.0029432 pmid: 22328917
[15]	KRAAKAMN A T W, NIKS R E, VAN DEN BERG P M M M, STAM P, EEUWIJK V. Linkage disequilibrium mapping of yield and yield stability in modern spring barley cultivars.Genetics, 2004, 168(1): 435-446. doi: 10.1534/genetics.104.026831 pmid: 15454555
[16]	YAN J B, KANDIANI C B, HARJES C E, KIM E H, YANG X, SKINNER D J, FU Z, MITCHELL S, LI Q, FERNANDEZ M G, ZAHARIEVA M, BABU R, FU Y, PALACIOS N, LI J, DELLAPENNA D, BRUTNELL T, BUCKLER E S, WARBURTON M L, ROCHEFORD T.Rare genetic variation at Zea mays crtRB1 increases beta-carotene in maize grain. Nature Genetic, 2010, 42(4): 322-327.
[17]	BRESEGHELLO F, SORRELLS M E.Association mapping of kernel size and milling quality in wheat (Triticum aestivum L.) cultivars. Genetics, 2006, 172: 1165-1177. doi: 10.1534/genetics.105.044586 pmid: 16079235
[18]	MASSMAN J, COOPER B, HORSLEY R, NEATE S, MACKY D, CHAO S, DONG Y, SCHWARZ P, MUEHIBAUER G L, SMITH K P.Genome-wide association mapping of Fusarium head blight resistance in contemporary barley breeding germplasm. Molecular Breeding, 2011, 27: 439-454. doi: 10.1007/s11032-010-9442-0
[19]	ROY J K, SMITH K P, MUEHLBAUER G J, CHAO S, CLOSE T J, STEFFENSON B J.Association mapping of spot blotch resistance in wild barley.Molecular Breeding, 2010, 26: 243-256. doi: 10.1007/s11032-010-9402-8 pmid: 20694035
[20]	ANDERSEN J R, LUBBERSTEDT T.Functional markers in plants, trends.Plant Science, 2003, 8(11): 554-560.
[21]	LIU Y N, HE Z H, APPELS R, XIA X C.Functional markers in wheat: current status and future prospects.Theoretical and Applied Genetic, 2012, 125: 1-10. doi: 10.1007/s00122-012-1829-3 pmid: 22366867
[22]	HAO C Y, DONG Y C, WANG L Y, YOU G X, ZHANG H N, GE H M, JIA J Z, ZHANG X Y.Genetic diversity and construction of core collection in Chinese wheat genetic resources.Chinese Science Bulletin, 2008, 53: 1518-1526. doi: 10.1007/s11434-008-0212-x
[23]	LIVAK K J, SCHMITTGEN T D.Analysis of relative gene expression data using real-time quantitative PCR and the 2 (-Delta Delta C (T) ) method.Methods, 2001, 25: 402-408.
[24]	刘秀林, 昌小平, 李润植, 景蕊莲. 小麦种子根结构及胚芽鞘长度的QTL分析的方法. 作物学报, 2011, 37(3): 381-388. doi: 10.3724/SP.J.1006.2011.00381
	LIU X L, CHANG X P, LI R Z, JING R L.Mapping QTLs for seminal root architecture and coleoptile length in wheat.Acta Agronomica Sinica, 2011, 37(3): 381-388. (in Chinese) doi: 10.3724/SP.J.1006.2011.00381
[25]	BRADBURY P J, ZHANG Z, KROON D E, CASSTEVENS T M, RAMDOSS Y, BUCHLER E S.TASSEL: Software for association mapping of complex traits in diverse samples.Bioinformatics, 2007, 23: 2633-2635. doi: 10.1093/bioinformatics/btm308 pmid: 17586829
[26]	LIAO H, YAN X L.Adaptive changes and geno-typic variation of root architecture of common bean in response to phosphorus deficiency.Acta Botanica Sinica, 2000, 42(2): 158-163.
[27]	郝留根. 小麦根系性状测定方法的比较及根系性状的QTL分析[D]. 杨凌: 西北农林科技大学, 2014.
	HAO L G.Comparison on different methods for measuring root traits and QTL analysis on root traits in wheat [D]. Yangling: Northwest Agriculture and Forestry University, 2014. (in Chinese)
[28]	刘士哲. 无土栽培技术. 北京: 中国农业出版社, 200l.
	LIU S Z. Soilless Planting Technique.Beijing: China Agriculture Press, 2001. (in Chinese)
[29]	张喜英. 作物根系与土壤水利用. 北京: 气象出版社, 1999.
	ZHANG X Y.Crop Roots and Soil Moisture Utilization. Beijing: Meteorological Press, 1999. (in Chinese)
[30]	李维炯. 测定根生物量的简便方法-土钻法. 耕作与栽培, 1984(6): 43.
	LI W J.Methods of studying roots systems of auger.Tillage and Cultivation, 1984(6): 43. (in Chinese)
[31]	杨丽雯, 张永清. 4种旱作谷类作物根系发育规律的研究. 中国农业科学, 2011, 44(11): 2244-2251. doi: 10.3864/j.issn.0578-1752.2011.11.005
	YANG L W, ZHANG Y Q.Developing patterns of root systems of four cereal crops planted in dryland areas.Scientia Agricultura Sinica, 2012, 44(11): 2244-2251. (in Chinese) doi: 10.3864/j.issn.0578-1752.2011.11.005
[32]	JOHNSON M G, TINGEY D T, PHILLIPS D L, STORM M J.Advancing fine root research with minirhizotrons.Environmental and Experimental Botany, 2001, 45(3): 263-289. doi: 10.1016/S0098-8472(01)00077-6 pmid: 11323033
[33]	LI B, LI Q R, MAO X G, LI A, WANG J Y, CHANG X P, HAO C Y, ZHANG X Y,JING R . Two novel AP2/EREBP transcription factor genes TaPARG have pleiotropic functions on plant architecture and yield-related traits in common wheat. Plant Science, 2016, 7: 1191. doi: 10.3389/fpls.2016.01191 pmid: 4977303
[34]	ABE J, MORITA S.Growth direction of nodal roots in rice: its variation and contribution to root system formation.Plant Soil, 1994, 165: 333-337. doi: 10.1007/BF00008078
[35]	ARAKI H, MORITA S, TATSUMI J, IIJIMA M.Physio- morphological analysis on axile root growth in upland rice.Plant Production Science, 2002, 5: 286-293.
[36]	YOSHIDA S, HASEGAWA S.The rice root system: its development and function//Drought Resistance in Crops with Emphasis on Rice. Manila: International Rice Research Institute, 1982: 97-114.
[37]	FUKAI S, COOPER M.Development of drought-resistant cultivars using physio-morphological traits in rice.Field Crops Research, 1995, 40: 67-86. doi: 10.1016/0378-4290(94)00096-U
[38]	RICH S M, WATT M.Soil conditions and cereal root system architecture: Review and considerations for linking Darwin and Weaver.Journal of Experimental Botany, 2013, 64: 1193-1208. doi: 10.1093/jxb/ert043 pmid: 23505309
[39]	WASSON A P, RICHARD R A, CHATRATH R, MISRA S C, PRASAD S V, REBETZKE G J, KIRKEGAARD J A, CHRISTOPHER J, WALT M.Traits and selection strategies to improve root systems and water uptake in water-limited wheat crops.Journal of Experimental Botany, 2012, 63(9): 3485-3498. doi: 10.1093/jxb/ers111 pmid: 22553286
[40]	MANSCHADI A M, CHRISTOPHER J T, VOIL P D, HAMMER G L.The role of root architectural traits in adaptation of wheat to water-limited environments.Functional Plant Biology, 2006, 33: 823-837. doi: 10.1071/FP06055
[41]	KIRKEGAARD J A, LILLEY J M, HOWE G N, GRAHMA J M.Impact of subsoil water use on wheat yield.Australian Journal Agricultural Research, 2007, 58: 303-315.
[42]	于福来, 方玉强, 王文全, 王秋玲, 刘凤波. 甘草栽培群体主要数量性状遗传变异及相互关系研究.中国中药杂志, 2011, 36(18): 2457-2461. doi: 10.4268/cjcmm20111801
	YU F L, FANG Y Q, WANG W Q, WANG Q L, LIU F B.Genetic variability and interrelationships of mainly quantitative traits in Glycyrrhiza uralensis cultivated population. China Journal of Chinese Medica, 2011, 36(18): 2457-2461. (in Chinese) doi: 10.4268/cjcmm20111801
[43]	农田灌溉面积达8.77亿亩,占全国耕地面积的48% [EB/OL]. .
	The irrigated area of farmland is 877 million mu, accounting for 48% of the total arable land [EB/OL]. (in Chinese)
[44]	YUSAKU U, HANZAWA E, NAGAI S, SASAKI K, YANO M, SATO T.Identification of qSOR1, a major rice QTL involved in soil-surface rooting in paddy fields. Theoretical and Applied Genetics, 2011, 124(1): 75-86.
[45]	YUSAKU U, OKUNO K, YANO M.Dro1, a major QTL involved in deep rooting of rice under upland field conditions. Journal Experimental Botany, 2011, 62(8): 2485-2494. doi: 10.1093/jxb/erq429 pmid: 21212298
[46]	YUSAKU U, YAMAMOTO E, KANNO N, KAWAI S, MIZUBAYASHI T, FUKUOKA S.A major QTL controlling deep rooting on rice chromosome 4.Scientific Reports, 2013, 3: 3040. doi: 10.1038/srep03040 pmid: 24154623
[47]	YUSAKU U, KITOMI Y, YAMAMOTO E, KANNO N, KAWAI S, MIZUBAYASHI T, FUKUOKA S, A QTL for root growth angle on rice chromosome 7 is involved in the genetic pathway of DEEPER ROOTING 1. Rice, 2015, 8: 8. doi: 10.1186/s12284-015-0044-7 pmid: 4384719
[48]	WRIGHT S I, VROH I, SCHROEDER S, YASANORI M, DOEBLEY J, MCMULLEN M D, GAUT B S.The effects of artificial selection on the maize genome.Science, 2004, 308(5726): 1310-1314.
[49]	OLSEN K M, URUGGANAN M D.Molecular evidence on the origin and evolution of glutinous rice.Genetics, 2002, 162: 941-950.
[50]	PENG J, RICHARDS D E, HARTLEY N M, MURPHY G P, DEVOS K M, FLINTHAM J E, BEALES J, FISH L J, WORLAND A J, PELICA F, SUDHAKAR D, CHRISTOU P, SNAPE J W, GALE M D, HARBERD N P.Green revolution genes encode mutant gibberellin response modulators.Nature, 1999, 400(6741): 256-261.
[51]	FRARY A, NESBITT T C, GRANDILLO S, KNAAP E, CONG B, LIU J, MELLER J, ELBER R, ALPERT K B, TANKSLEY S D.fw2.2: A quantitative trait locus key to the evolution of tomato fruit size. Science, 2000, 289(5746): 85-88.
[52]	FAY J C, WU C I.Hitchhiking under positive Darwinian selection.Genetics, 2000, 155: 1405-1413. doi: 10.1002/1098-2272(200007)19:1<81::AID-GEPI6>3.0.CO;2-8 pmid: 10880498
[53]	WAINES J G, EHDAIE B.Domestication and crop physiology: Roots of Green-revolution wheat.Annals of Botany, 2007, 100(5): 991-998. doi: 10.1140/epjc/s2006-02484-y pmid: 17940075

年份 Year	地点 Site	环境 Environments	TaDRO-5A
年份 Year	地点 Site	环境 Environments	株高PH P-value	千粒重TKW P-value	根角度RGA P-value	株高PH P-value	根角度RGA P-value
2015	顺义 Shunyi	水WW	ns	ns		0.0017**
		旱DS	ns	0.0431*		ns
		水热HE	0.0310*	0.0252*		0.0011**
		旱热DE	0.0165*	0.0209*		0.0223*
2016	昌平 Changping	水WW	0.0223*	ns		0.0364*
	昌平 Changping	旱DS	ns	ns		0.0017**
	顺义 Shunyi	水WW	0.0160*	0.0342*		0.0133*
		旱DS	0.0148*	0.0198*		0.0327*
		水热HE	0.0108*	ns		0.0095**
		旱热DE	0.0243*	ns		0.0122*
2016	实验室 Lab				0.04984*		ns

性状 Trait	TaDRO-5A		TaDRO-5B
性状 Trait	Hap-5A-A	Hap-5A-C	Hap-5B-Ⅰ	Hap-5B-Ⅱ
根长RL	391.07±111.56	403.21±95.13	410.91±98.80a	383.97±112.15b
株高PH	116.85±23.22B	126.30±18.53A	130.20±13.34A	111.69±24.64B
千粒重TKW	41.50±7.49A	36.77±7.66B	35.99±6.58B	43.32±7.56A
根夹角RGA	112.87±1.39a	102.61±4.66b	112.10±3.64	111.73±1.46