利用BSA法发掘野生大豆种子硬实性相关QTL
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摘要
【目的】野生大豆的硬实性是大豆遗传改良利用中的重要限制因素。利用BSA法发掘与大豆种子硬实性相关的QTL,为野生大豆在大豆遗传改良中的合理利用奠定基础。【方法】利用栽培大豆中黄39与野生大豆NY27-38杂交构建F_2和F_7分离群体,从每个单株选取整齐一致的种子,取30粒种子置于铺有一层滤纸的培养皿中,加入30 mL蒸馏水,25℃培养箱中暗处理4 h,设3次重复,分别统计每个培养皿中正常吸胀和硬实种子数。在F_2群体中,选取22个正常吸胀单株(吸胀率>90%)和16个硬实单株(吸胀率<10%);在F_7群体中,选取20个完全吸胀单株(吸胀率=100%)和20个完全硬实单株(吸胀率=0%),单株DNA等量混合,分别构建2个吸胀和2个硬实DNA池。利用259对在亲本间有多态性的SSR标记对吸胀和硬实DNA池进行检测,筛选在吸胀和硬实DNA池间表现多态性的SSR标记;用192个SSR标记检测F_7分离群体,构建遗传图谱,利用复合区间作图法定位大豆硬实相关QTL。【结果】利用F_2个体构建的吸胀和硬实DNA池,在第2染色体16.3 Mb区间和第6染色体23.4 Mb区间分别检测到10个和8个在两池间有差异的SSR标记。利用这些标记检测F_2群体,将第2染色体的QTL定位于Satt274与Sat_198间的276.0 kb区间,该区间包括已克隆的大豆硬实基因GmHs1-1,解释17.2%的表型变异。第6染色体的QTL位于标记BARCSOYSSR_06_0993与BARCSOYSSR_06_1068间,可解释17.8%的表型变异。利用F_7株系构建的吸胀和硬实DNA池,在第2(27.4 Mb区间)、6(27.8 Mb区间)和3染色体(18.2 Mb区间)分别检测到11个、9个和4个在两池间有多态性的SSR标记。利用F_7群体构建包括192个SSR标记、覆盖2 390.2 cM的遗传图谱,共检测到3个硬实相关QTL,其中第2染色体定位到的QTL位于标记Satt274与Sat_198间,可解释23.3%的遗传变异。第6染色体定位到的QTL位于标记Sat_402与Satt557之间,可解释20.4%的表型变异。在第3染色体标记Sat_266与Sat_236间发现一个可以解释4.9%表型变异的QTL,与BSA法检测的结果相符。【结论】利用BSA法可以检测到传统遗传作图定位的所有与硬实性相关的QTL,证明BSA法发掘大豆种子硬实性主要QTL的高效性。
【Objective】 Hard seededness of wild soybean is an important effector that limits the utilization of wild resources in soybean genetic improvement. Bulked segregant analysis(BSA) was employed to identify major quantitative trait loci(QTLs)related with hard seededness in soybean, which laid a foundation for effective utilization of wild soybean germplasm in cultivated soybean improvement. 【Method】 F_2 and F_7 segregation populations were constructed from a cross between cultivated soybean Zhonghuang39 and wild soybean NY27-38. Uniformly sized seeds were selected from each line, and 30 seeds were soaked in a petri dish with 30 mL distilled water for 4 hours at 25℃. The assay was replicated 3 times. The number of permeable and impermeable seeds were counted. In F_2 population, the first DNA pool was constructed from 22 individuals with permeable seeds(imbibition rate>90%), and second DNA pool was constructed from 16 individuals with impermeable seeds(imbibition rate <10%). In F_7 population, 20 lines with permeable seeds(100% imbibition) and 20 lines with impermeable seeds(no imbibition) were used to construct two DNA pools, respectively. To detect genomic regions associated with hard seededness, these DNA bulks were genotyped with 259 polymorphic SSR markers to identify markers linked to QTL. A linkage map was constructed with 192 SSR markers, QTLs related with hard seededness were identified by composite interval mapping in F_7 segregation population. 【Result】Out of 259 SSR loci polymorphic between Zhonghuang39 and NY27-38, 10 and eight polymorphic SSR markers between the permeable and impermeable pools were detected in 16.3 Mb interval on chromosome 2 and 23.4 Mb interval on chromosome 6,respectively, in F_2 population. The QTL region(276.0 kb) located between Satt274 and Sat_198 on chromosome 2 contained previously cloned gene Gm Hs1-1, the QTL explained 17.2% of the total genetic variation. The other QTL was mapped on chromosome 6 flanked by BARCSOYSSR_06_0993 and BARCSOYSSR_06_1068, accounting for 17.8% of the total genetic variation. In F_7 population, eleven, nine and four SSR polymorphic markers between the permeable and impermeable pools were detected in 27.4 Mb interval on chromosome 2, 27.8 Mb interval on chromosome 6, 18.2 Mb interval on chromosome 3, respectively.A linkage map of 192 SSR markers and covering 2 390.2 cM was constructed through composite interval mapping in F_7 population.Three QTLs related with hard seededness were detected. The QTL on chromosome 2 located between Satt274 and Sat_198,explained 23.3% of the total genetic variation; the QTL on chromosome 6 flanked by Sat_402 and Satt557, explained 20.4% of the total genetic variation; the QTL on chromosome 3 flanked by Sat_266 and Sat_236 accounted for 4.9% of the total genetic variation.【Conclusion】In this study, three QTLs related to soybean hard seededness were identified by both BSA and traditional linkage mapping, indicating that BSA is an effective strategy for identifying QTLs in soybean.
【Objective】 Hard seededness of wild soybean is an important effector that limits the utilization of wild resources in soybean genetic improvement. Bulked segregant analysis(BSA) was employed to identify major quantitative trait loci(QTLs)related with hard seededness in soybean, which laid a foundation for effective utilization of wild soybean germplasm in cultivated soybean improvement. 【Method】 F_2 and F_7 segregation populations were constructed from a cross between cultivated soybean Zhonghuang39 and wild soybean NY27-38. Uniformly sized seeds were selected from each line, and 30 seeds were soaked in a petri dish with 30 mL distilled water for 4 hours at 25℃. The assay was replicated 3 times. The number of permeable and impermeable seeds were counted. In F_2 population, the first DNA pool was constructed from 22 individuals with permeable seeds(imbibition rate>90%), and second DNA pool was constructed from 16 individuals with impermeable seeds(imbibition rate <10%). In F_7 population, 20 lines with permeable seeds(100% imbibition) and 20 lines with impermeable seeds(no imbibition) were used to construct two DNA pools, respectively. To detect genomic regions associated with hard seededness, these DNA bulks were genotyped with 259 polymorphic SSR markers to identify markers linked to QTL. A linkage map was constructed with 192 SSR markers, QTLs related with hard seededness were identified by composite interval mapping in F_7 segregation population. 【Result】Out of 259 SSR loci polymorphic between Zhonghuang39 and NY27-38, 10 and eight polymorphic SSR markers between the permeable and impermeable pools were detected in 16.3 Mb interval on chromosome 2 and 23.4 Mb interval on chromosome 6,respectively, in F_2 population. The QTL region(276.0 kb) located between Satt274 and Sat_198 on chromosome 2 contained previously cloned gene Gm Hs1-1, the QTL explained 17.2% of the total genetic variation. The other QTL was mapped on chromosome 6 flanked by BARCSOYSSR_06_0993 and BARCSOYSSR_06_1068, accounting for 17.8% of the total genetic variation. In F_7 population, eleven, nine and four SSR polymorphic markers between the permeable and impermeable pools were detected in 27.4 Mb interval on chromosome 2, 27.8 Mb interval on chromosome 6, 18.2 Mb interval on chromosome 3, respectively.A linkage map of 192 SSR markers and covering 2 390.2 cM was constructed through composite interval mapping in F_7 population.Three QTLs related with hard seededness were detected. The QTL on chromosome 2 located between Satt274 and Sat_198,explained 23.3% of the total genetic variation; the QTL on chromosome 6 flanked by Sat_402 and Satt557, explained 20.4% of the total genetic variation; the QTL on chromosome 3 flanked by Sat_266 and Sat_236 accounted for 4.9% of the total genetic variation.【Conclusion】In this study, three QTLs related to soybean hard seededness were identified by both BSA and traditional linkage mapping, indicating that BSA is an effective strategy for identifying QTLs in soybean.
引文
[1]孙星邈,王政,李曙光,孟凡凡,王曙明,张井勇.大豆硬实形成机制与破除技术的研究进展.大豆科技,2014(3):23-27.SUN X M,WANG Z,LI S G,MENG F F,WANG S M,ZHANG J Y.Progress on formation mechanism and breaking methods of hard seeds in soybean.Soybean Science Technology,2014(3):23-27.(in Chinese)
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[3]MOHAMED Y Y,BARRINGER S A,SPLITTSTOESSER W E.The role of seed coats in seed viability.The Botanical Review,1994,60(4):426-439.
[4]POTTS H C,DUANGPATRA J,HAIRSTON W G.Some influences of hard seededness on soybean seed quality.Crop Science,1978,18(2):221-224.
[5]HEATHERLY L G,KENTY M M,KILEN T C.Effects of storage environment and duration on impermeable seed coat in soybean.Field Crops Research,1995,40(1):57-62.
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[9]HARRIS W M.Comparative ultrastructure of developing seed coats of“hard-seeded”and“soft-seeded”varieties of soybean,Glycine max(L.)Merr.Botanical Gazette,1987,148(3):324-331.
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[14]LIU B,FUJITA T,YAN Z H,SAKAMOTO S.QTL mapping of domestication-related traits in soybean(Glycine max).Annals of Botany,2007,100(5):1027-1038.
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[21]MANSUR L M,ORF J,LARF K G.Determining the linkage of quantitative trait loci to RFLP markers using extreme phenotypes of recombinant inbreds of soybean(Glycine max L.Merr.).Theoretical and Applied Genetics,1993,86(8):914-918.
[22]HAYES A J,MA G,BUSS G R,MAROOF M A S.Molecular marker mapping of Rsv4,a gene conferring resistance to all known strains of soybean mosaic virus.Crop Science,2000,40(5):1434-1437.
[23]ZHAO G,ABLETT G R,ANDERSON T R,RAJCAN I,SCHAAFSMA A W.Inheritance and genetic mapping of resistance to rhizoctonia root and hypocotyl rot in soybean.Crop Science,2005,45(4):1441-1447.
[24]SILVA D C G,YAMANAKA N,BROGIN R L,ARIAS C A A,NEPOMUCENO A L,MAURO A O D,PEREIRA S S,NOGUEIRAL M,PASSIANOTTO A L L,ABDELNOOR R V.Molecular mapping of two loci that confer resistance to Asian rust in soybean.Theoretical and Applied Genetics,2008,117(1):57-63.
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[26]SUN J T,LI L H,ZHAO J M,HUANG J,YAN Q,XING H,GUO N.Genetic analysis and fine mapping of RpsJS,a novel resistance gene to Phytophthora sojae in soybean[Glycine max(L.)Merr.].Theoretical and Applied Genetics,2014,127(4):913-919.
[27]蒙忻,刘学义,方宣钧.利用大豆分子连锁图定位大豆孢囊线虫4号生理小种抗性QTL.分子植物育种,2003,1(1):6-21.MENG X,LIU X Y,FANG X J.QTL mapping genes conferring resistance to race 4 of soybean cyst nematode in soybean ZDD2315(Glycine max(L.)Merr.)based on public molecular genetic linkage map.Molecular Breeding of Plant,2003,1(1):6-21.(in Chinese)
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[2]李向华,王克晶,李福山,严茂粉.野生大豆(Glycine soja)研究现状与建议.大豆科学,2005,24(4):305-309.LI X H,WANG K J,LI F S,YAN M F.Research progress of wild soybean(Glycine soja)and suggestions for improving its effective utilization and protection.Soybean Science,2005,24(4):305-309.(in Chinese)
[3]MOHAMED Y Y,BARRINGER S A,SPLITTSTOESSER W E.The role of seed coats in seed viability.The Botanical Review,1994,60(4):426-439.
[4]POTTS H C,DUANGPATRA J,HAIRSTON W G.Some influences of hard seededness on soybean seed quality.Crop Science,1978,18(2):221-224.
[5]HEATHERLY L G,KENTY M M,KILEN T C.Effects of storage environment and duration on impermeable seed coat in soybean.Field Crops Research,1995,40(1):57-62.
[6]牛连杰.浅析种子发生硬实的原因及影响硬实形成的因素.种子世界,2004,9:32.NIU L J.Causes of hard seededness and factors affecting the formation of hard seededness.Seed World,2004,9:32.(in Chinese)
[7]徐亮,李建东,殷萍萍,王国骄,燕雪飞,孙备.野生大豆种皮形态结构和萌发特性的研究.大豆科学,2009,28(4):641-646.XU L,LI J D,YIN P P,WANG G J,YAN X F,SUN B.Test a morphology structure and germination characteristic of wild soybean(Glycine soja).Soybean Science,2009,28(4):641-646.(in Chinese)
[8]MA F,CHOLEWA E W A,MOHAMED T,PETERSON C A,GIJZEN M.Cracks in the palisade cuticle of soybean seed coats correlate with their permeability to water.Annals of Botany,2004,94(2):213-228.
[9]HARRIS W M.Comparative ultrastructure of developing seed coats of“hard-seeded”and“soft-seeded”varieties of soybean,Glycine max(L.)Merr.Botanical Gazette,1987,148(3):324-331.
[10]郭彪,雷金芝,马景林.大豆硬实的形成及不同品种硬实率调查.现代化农业,2002(7):6-7.GUO B,LEI J Z,MA J L.Investigation on formation of soybean hard seededness and hard seededness rate of different varieties.Modern Agriculture,2002(7):6-7.(in Chinese)
[11]KEIM P,DIERS B W,SHOEMAKER R C.Genetic analysis of soybean hard seededness with molecular markers.Theoretical and Applied Genetics,1990,79(4):465-469.
[12]SAKAMOTO S,ABE J,KANAZAWA A,SHIMAMOTO Y.Markerassisted analysis for soybean hard seededness with isozyme and simple sequence repeat loci.Breeding Science,2004,54(2):133-139.
[13]WATANABE S,TAJUDDIN T,YAMANAKA N,HAYASHI M,HARADA K.Analysis of QTLs for reproductive development and seed quality traits in soybean using recombinant inbred lines.Breeding Science,2004,54(4):399-407.
[14]LIU B,FUJITA T,YAN Z H,SAKAMOTO S.QTL mapping of domestication-related traits in soybean(Glycine max).Annals of Botany,2007,100(5):1027-1038.
[15]SINGH R K,RAIPURIA R K,BHATIA V S,RANI A,PUSHPENDRA,HUSAIN S M,SATYAVATHI C T,CHAUHAN G S,MOHAPATRA T.Identification of SSR markers associated with seed coat permeability electrolyte leaching in soybean.Physiology and Molecular Biology of Plants,2008,14(3):173-177.
[16]KEBEDE H,SMITH J R,RAY J D.Identification of a single gene for seed coat impermeability in soybean PI 594619.Theoretical and Applied Genetics,2014,127(9):1991-2003.
[17]艾丽娟,陈强,杨春燕,闫龙,王凤敏,葛荣朝,张孟臣.大豆籽粒硬实加性和上位性QTL定位.作物学报,2018,44(6):852-858.AI L J,CHEN Q,YANG C Y,YAN L,WANG F M,GE R C,ZHANGM C.Additive and epistatic QTL mapping for soybean hard seededness.Acta Agronomica Sinica,2018,44(6):852-858.(in Chinese)
[18]JANG S J,SATO M,SATO K,JILSUYAMA Y,FUJINO K,MORI H,TAKAHASHI R,BENITEZ E R,LIU B H,YAMADA T,ABE J.Asingle-nucleotide polymorphism in an endo-1,4-β-glucanase gene controls seed coat permeability in soybean.PLoS ONE,2015,10(6):e0128527.
[19]SUN L J,MIAO Z Y,CAI C M,ZHANG D J,ZHAO M X,WU Y Y,ZHANG X L,SWARM S A,ZHOU L W,ZHANG Z Y,NELSON R L,MA J X.Gm Hs1-1,encoding a calcineurin-like protein,controls hard seededness in soybean.Nature Genetics,2015,47(8):939-943.
[20]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 USA,1991,88(21):9828-9832.
[21]MANSUR L M,ORF J,LARF K G.Determining the linkage of quantitative trait loci to RFLP markers using extreme phenotypes of recombinant inbreds of soybean(Glycine max L.Merr.).Theoretical and Applied Genetics,1993,86(8):914-918.
[22]HAYES A J,MA G,BUSS G R,MAROOF M A S.Molecular marker mapping of Rsv4,a gene conferring resistance to all known strains of soybean mosaic virus.Crop Science,2000,40(5):1434-1437.
[23]ZHAO G,ABLETT G R,ANDERSON T R,RAJCAN I,SCHAAFSMA A W.Inheritance and genetic mapping of resistance to rhizoctonia root and hypocotyl rot in soybean.Crop Science,2005,45(4):1441-1447.
[24]SILVA D C G,YAMANAKA N,BROGIN R L,ARIAS C A A,NEPOMUCENO A L,MAURO A O D,PEREIRA S S,NOGUEIRAL M,PASSIANOTTO A L L,ABDELNOOR R V.Molecular mapping of two loci that confer resistance to Asian rust in soybean.Theoretical and Applied Genetics,2008,117(1):57-63.
[25]GARCIA A,CALVO E S,KIIHL R A D S,HARADA A,HIROMOTO D M,VIEIRA L G E.Molecular mapping of soybean rust(Phakopsora pachyrhizi)resistance genes:discovery of a novel locus and alleles.Theoretical and Applied Genetics,2008,117(4):545-553.
[26]SUN J T,LI L H,ZHAO J M,HUANG J,YAN Q,XING H,GUO N.Genetic analysis and fine mapping of RpsJS,a novel resistance gene to Phytophthora sojae in soybean[Glycine max(L.)Merr.].Theoretical and Applied Genetics,2014,127(4):913-919.
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