Genetic dissection of hexanol content in soybean seed through genome-wide association analysis
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摘要
Hexanol is a major compound contributing to the off-flavors(the bean-like odor) of soybean derived soymilk. The most effective way to reduce the off-flavors of soymilk is the screening and utilization of soybean cultivars with improved hexanol content. However, no genome-wide genetic analysis for this particular trait has been conducted to date. The objective of the present study was to dissect the genetic basis of hexanol content in soybean seed through genome-wide association analysis(GWAS). A total of 105 soybean accessions were analyzed for hexanol content in a three-year experiments and genotyped by sequencing using the specific locus amplified fragment sequencing(SLAF-seq) approach. A total of 25 724 single nucleotide polymorphisms(SNPs) were obtained with minor allele frequencies(MAF)>5%. GWAS showed that 25 quantitative trait nucleotides(QTNs) were significantly associated with the hexanol concentration in soybean seed. These identified QTNs distributed on different genomic regions of the 15 chromosomes. A total of 91 genes were predicted as candidate genes underlying the seed hexanol level and six candidates were predicted possibly underlying the seed hexanol by gene based association. In this study, GWAS has been proven to be an effective way to dissect the genetic basis of the hexanol concentration in multiple genetic backgrounds. The identified beneficial alleles and candidate genes might be valuable for the improvement of marker-assisted breeding efficiency for low hexanol level and help to explore possible molecular mechanisms underlying hexanol content in soybean seed.
Hexanol is a major compound contributing to the off-flavors(the bean-like odor) of soybean derived soymilk. The most effective way to reduce the off-flavors of soymilk is the screening and utilization of soybean cultivars with improved hexanol content. However, no genome-wide genetic analysis for this particular trait has been conducted to date. The objective of the present study was to dissect the genetic basis of hexanol content in soybean seed through genome-wide association analysis(GWAS). A total of 105 soybean accessions were analyzed for hexanol content in a three-year experiments and genotyped by sequencing using the specific locus amplified fragment sequencing(SLAF-seq) approach. A total of 25 724 single nucleotide polymorphisms(SNPs) were obtained with minor allele frequencies(MAF)>5%. GWAS showed that 25 quantitative trait nucleotides(QTNs) were significantly associated with the hexanol concentration in soybean seed. These identified QTNs distributed on different genomic regions of the 15 chromosomes. A total of 91 genes were predicted as candidate genes underlying the seed hexanol level and six candidates were predicted possibly underlying the seed hexanol by gene based association. In this study, GWAS has been proven to be an effective way to dissect the genetic basis of the hexanol concentration in multiple genetic backgrounds. The identified beneficial alleles and candidate genes might be valuable for the improvement of marker-assisted breeding efficiency for low hexanol level and help to explore possible molecular mechanisms underlying hexanol content in soybean seed.
Hexanol is a major compound contributing to the off-flavors(the bean-like odor) of soybean derived soymilk. The most effective way to reduce the off-flavors of soymilk is the screening and utilization of soybean cultivars with improved hexanol content. However, no genome-wide genetic analysis for this particular trait has been conducted to date. The objective of the present study was to dissect the genetic basis of hexanol content in soybean seed through genome-wide association analysis(GWAS). A total of 105 soybean accessions were analyzed for hexanol content in a three-year experiments and genotyped by sequencing using the specific locus amplified fragment sequencing(SLAF-seq) approach. A total of 25 724 single nucleotide polymorphisms(SNPs) were obtained with minor allele frequencies(MAF)>5%. GWAS showed that 25 quantitative trait nucleotides(QTNs) were significantly associated with the hexanol concentration in soybean seed. These identified QTNs distributed on different genomic regions of the 15 chromosomes. A total of 91 genes were predicted as candidate genes underlying the seed hexanol level and six candidates were predicted possibly underlying the seed hexanol by gene based association. In this study, GWAS has been proven to be an effective way to dissect the genetic basis of the hexanol concentration in multiple genetic backgrounds. The identified beneficial alleles and candidate genes might be valuable for the improvement of marker-assisted breeding efficiency for low hexanol level and help to explore possible molecular mechanisms underlying hexanol content in soybean seed.
引文
Achouri A,Boye J I,Zamani Y.2006.Identification of volatile compounds in soymilk using solid-phase microextractiongas chromatography.Food Chemistry,99,759-766.
Arai S,Kbayashi A,Yajima I,Kawasaki M.2000.SaishinKoryonojiten.Asakurashoten,Tokyo,Japan.p.387.
Arai S,Koyanagi O,Fujimaki M.1967.Studies on flavor compounds in soybean,part IV.Volatile neutral compounds.Agriculrural Biological Chemistry,31,868-873.
Bachlava E,Dewey R E,Burton J W,Cardinal A J.2009.Mapping and comparison of quantitative trait loci for oleic acid seed content in two segregating soybean populations.Crop Science,49,433-442.
Bradbury P J,Zhang Z,Kroon D E,Casstevens T M,Ramdoss Y,Buckler E S.2007.TASSEL:Software for association mapping of complex traits in diverse samples.Bioinformatics,23,2633-2635.
Chen H T,Liu X Q,Zhang H M,Yuan X X,Gu H P,Cui X Y,Chen X.2018.Advances in salinity tolerance of soybean:genetic diversity,heredity,and gene identification contribute to improving salinity tolerance.Journal of Integrative Agriculture,17,83-89.
Cheng P,Gedling C R,Patil G,Vuong T D,Shannon J G,Dorrance A E,Nguyen H T.2017.Genetic mapping and haplotype analysis of a locus for quantitative resistance to Fusarium graminearum in soybean accession PI 567516C.Theoretical and Applied Genetics,130,999-1010.
Guo B,Sleper D A,Nguyen H T,Arelli P R,Shannon J G.2006.Quantitative trait loci underlying resistance to three soybean cyst nematode populations in soybean PI 404198A.Crop Science,46,224-233.
Han Y,Zhao X,Cao G,Wang Y,Li Y,Liu D,Teng W,Zhang Z,Li D,Qiu L.2015.Genetic characteristics of soybean resistance to HG type 0 and HG type 1.2.3.5.7 of the cyst nematode analyzed by genome-wide association mapping.BMC Genomics,16,598.
Hwang E,Song Q,Jia G,Specht J,hyuten D,Costa J,Cregan P.2014.A genome-wide association study of seed protein and oil content in soybean.BMC Genomics,15,1.
Kabelka E A,Diers B W,Fehr W R,LeRoy A R,Baianu I C,You T,Neece D J,Nelson R L.2004.Putative alleles for increased yield from soybean plant introductions.Crop Science,44,784-791.
Keast R,Lau J.2006.Culture-specific variation in the flavor profile of soymilks.Journal of Food Science,71,S567-S572.
Kim Y,Kim C.1999.Effects of extraction methods and heating times on physicochemical properties of soymilk.Korean Soybean Digest,16,40-55.
Kobayashi A,Tsuda Y,Hirata N,Kubota K,Kitamura K.1995.Aroma constituents of soybean[Glycine max(L.)Merril]milk lacking lipoxygenase isoenzymes.Journal of Agricultural and Food Chemistry,43,2449-2452.
Li R,Yu C,Li Y,Lam T W,Yiu S M,Kristiansen K,Wang J.2009.SOAP2:An improved ultrafast tool for short read alignment.Bioinformatics,25,1966-1967.
Li Y,Reif J,Ma Y,Hong H,Liu Z,Chang R,Qiu L.2015.Targeted association mapping demonstrating the complex molecular genetics of fatty acid formation in soybean.BMCGenomics,16,841.
Lipka A E,Tian F,Wang Q,Peiffer J,Li M,Bradbury P J,Gore M A,Buckler E S,Zhang Z.2012.GAPIT:Genome association and prediction integrated tool.Bioinformatics,28,2397-2399.
Lozano P R,Drake M,Benitez D,Cadwallader K R.2007.Instrumental and sensory characterization of heat-induced odorants in aseptically packaged soymilk.Journal of Agricultural and Food Chemistry,55,3018-3026.
Matoba T,Sakurai A,Taninoki N,Saitoh T,Kariya F,Kuwahara M,Yukawa N,Fujino S,Hasegawa K.1989.n-Hexanol formation from n-hexanal by enzyme action in soybean extracts.Journal of Food Science,54,1607-1610.
N’Kouka K D,Klein B P,Lee S.2004.Developing a lexicon for descriptive analysis of soymilks.Journal of Food Science,69,259-263.
Orthoefer F T,Liu K.1995.Soybeans for food uses.Food Mark Technology,9,4-8.
Poliseli-Scopel F H,Hernández-Herrero M,Guamis B,Ferragut V.2012.Comparison of ultra high pressure homogenization and conventional thermal treatments on the microbiological,physical and chemical quality of soymilk.LWT-Food Science and Technology,46,42-48.
Shi X D,Li J Y,Wang S M,Zhang L,Qiu L J,Han T F,Wang QY,Chang S,Guo S T.2015.Flavor characteristic analysis of soymilk prepared by different soybean cultivars and establishment of evaluation method of soybean cultivars suitable for soymilk processing.Food Chemistry,185,422-429.
Shibata M,Takayama K,Ujiie A,Yamada T,Abe J,Kitamura K.2008.Genetic relationship between lipid content and linolenic acid concentration in soybean seeds.Breed Science,58,361-366.
Sun X,Liu D,Zhang X,Li W,Liu H,Hong W,Jiang C,Guan N,Ma C,Zheng H.2013.SLAF-seq:An efficient method of large-scale de novo SNP discovery and genotyping using high-throughput sequencing.PLoS ONE,8,e58700.
Torres-Penaranda A V,Reitmeier C A.2001.Sensory descriptive analysis of soymilk.Journal of Food Science,66,352-356.
Vara-Ubol S,Chambers E,Chambers D H.2004.Sensory characteristics of chemical compounds potentially associated with beany aroma in foods.Journal of Sensory Studies,19,15-26.
Wilkens W,Lin F.1970.Gas chromatographic and mass spectral analyses of soybean milk volatiles.Journal of Agricultural and Food Chemistry,18,333-336.
Zhao X,Han Y,Li Y,Liu D,Sun M,Zhao Y,Lv C,Li D,Yang Z,Huang L,Teng W,Qiu L,Zheng H,Li W.2015.Loci and candidate gene identification for resistance to sclerotinia sclerotiorum in soybean(Glycine max L.Merr.)via association and linkage maps.Plant Journal for Cell&Molecular Biology,82,245-255.
Zhao X,Teng W,Li Y,Liu D,Gao G,Li D,Qiu L,Zheng H,Han Y,Li W.2017.Loci and candidate genes conferring resistance to soybean cyst nematode HG type 2.5.7.BMCGenomics,18,462.
Zhou Z,Jiang Y,Wang Z,Gou Z,Lyu J,Li W,Yu Y,Shu L,Zhao Y,Ma Y,Fang C,Shen Y,Liu T,Li C,Li Q,Wu M,Wang M,Wu Y,Dong Y,Wan W,et al.2015.Resequencing302 wild and cultivated accessions identifies genes related to domestication and improvement in soybean.Nature Biotechnology,33,408-414.
Arai S,Kbayashi A,Yajima I,Kawasaki M.2000.SaishinKoryonojiten.Asakurashoten,Tokyo,Japan.p.387.
Arai S,Koyanagi O,Fujimaki M.1967.Studies on flavor compounds in soybean,part IV.Volatile neutral compounds.Agriculrural Biological Chemistry,31,868-873.
Bachlava E,Dewey R E,Burton J W,Cardinal A J.2009.Mapping and comparison of quantitative trait loci for oleic acid seed content in two segregating soybean populations.Crop Science,49,433-442.
Bradbury P J,Zhang Z,Kroon D E,Casstevens T M,Ramdoss Y,Buckler E S.2007.TASSEL:Software for association mapping of complex traits in diverse samples.Bioinformatics,23,2633-2635.
Chen H T,Liu X Q,Zhang H M,Yuan X X,Gu H P,Cui X Y,Chen X.2018.Advances in salinity tolerance of soybean:genetic diversity,heredity,and gene identification contribute to improving salinity tolerance.Journal of Integrative Agriculture,17,83-89.
Cheng P,Gedling C R,Patil G,Vuong T D,Shannon J G,Dorrance A E,Nguyen H T.2017.Genetic mapping and haplotype analysis of a locus for quantitative resistance to Fusarium graminearum in soybean accession PI 567516C.Theoretical and Applied Genetics,130,999-1010.
Guo B,Sleper D A,Nguyen H T,Arelli P R,Shannon J G.2006.Quantitative trait loci underlying resistance to three soybean cyst nematode populations in soybean PI 404198A.Crop Science,46,224-233.
Han Y,Zhao X,Cao G,Wang Y,Li Y,Liu D,Teng W,Zhang Z,Li D,Qiu L.2015.Genetic characteristics of soybean resistance to HG type 0 and HG type 1.2.3.5.7 of the cyst nematode analyzed by genome-wide association mapping.BMC Genomics,16,598.
Hwang E,Song Q,Jia G,Specht J,hyuten D,Costa J,Cregan P.2014.A genome-wide association study of seed protein and oil content in soybean.BMC Genomics,15,1.
Kabelka E A,Diers B W,Fehr W R,LeRoy A R,Baianu I C,You T,Neece D J,Nelson R L.2004.Putative alleles for increased yield from soybean plant introductions.Crop Science,44,784-791.
Keast R,Lau J.2006.Culture-specific variation in the flavor profile of soymilks.Journal of Food Science,71,S567-S572.
Kim Y,Kim C.1999.Effects of extraction methods and heating times on physicochemical properties of soymilk.Korean Soybean Digest,16,40-55.
Kobayashi A,Tsuda Y,Hirata N,Kubota K,Kitamura K.1995.Aroma constituents of soybean[Glycine max(L.)Merril]milk lacking lipoxygenase isoenzymes.Journal of Agricultural and Food Chemistry,43,2449-2452.
Li R,Yu C,Li Y,Lam T W,Yiu S M,Kristiansen K,Wang J.2009.SOAP2:An improved ultrafast tool for short read alignment.Bioinformatics,25,1966-1967.
Li Y,Reif J,Ma Y,Hong H,Liu Z,Chang R,Qiu L.2015.Targeted association mapping demonstrating the complex molecular genetics of fatty acid formation in soybean.BMCGenomics,16,841.
Lipka A E,Tian F,Wang Q,Peiffer J,Li M,Bradbury P J,Gore M A,Buckler E S,Zhang Z.2012.GAPIT:Genome association and prediction integrated tool.Bioinformatics,28,2397-2399.
Lozano P R,Drake M,Benitez D,Cadwallader K R.2007.Instrumental and sensory characterization of heat-induced odorants in aseptically packaged soymilk.Journal of Agricultural and Food Chemistry,55,3018-3026.
Matoba T,Sakurai A,Taninoki N,Saitoh T,Kariya F,Kuwahara M,Yukawa N,Fujino S,Hasegawa K.1989.n-Hexanol formation from n-hexanal by enzyme action in soybean extracts.Journal of Food Science,54,1607-1610.
N’Kouka K D,Klein B P,Lee S.2004.Developing a lexicon for descriptive analysis of soymilks.Journal of Food Science,69,259-263.
Orthoefer F T,Liu K.1995.Soybeans for food uses.Food Mark Technology,9,4-8.
Poliseli-Scopel F H,Hernández-Herrero M,Guamis B,Ferragut V.2012.Comparison of ultra high pressure homogenization and conventional thermal treatments on the microbiological,physical and chemical quality of soymilk.LWT-Food Science and Technology,46,42-48.
Shi X D,Li J Y,Wang S M,Zhang L,Qiu L J,Han T F,Wang QY,Chang S,Guo S T.2015.Flavor characteristic analysis of soymilk prepared by different soybean cultivars and establishment of evaluation method of soybean cultivars suitable for soymilk processing.Food Chemistry,185,422-429.
Shibata M,Takayama K,Ujiie A,Yamada T,Abe J,Kitamura K.2008.Genetic relationship between lipid content and linolenic acid concentration in soybean seeds.Breed Science,58,361-366.
Sun X,Liu D,Zhang X,Li W,Liu H,Hong W,Jiang C,Guan N,Ma C,Zheng H.2013.SLAF-seq:An efficient method of large-scale de novo SNP discovery and genotyping using high-throughput sequencing.PLoS ONE,8,e58700.
Torres-Penaranda A V,Reitmeier C A.2001.Sensory descriptive analysis of soymilk.Journal of Food Science,66,352-356.
Vara-Ubol S,Chambers E,Chambers D H.2004.Sensory characteristics of chemical compounds potentially associated with beany aroma in foods.Journal of Sensory Studies,19,15-26.
Wilkens W,Lin F.1970.Gas chromatographic and mass spectral analyses of soybean milk volatiles.Journal of Agricultural and Food Chemistry,18,333-336.
Zhao X,Han Y,Li Y,Liu D,Sun M,Zhao Y,Lv C,Li D,Yang Z,Huang L,Teng W,Qiu L,Zheng H,Li W.2015.Loci and candidate gene identification for resistance to sclerotinia sclerotiorum in soybean(Glycine max L.Merr.)via association and linkage maps.Plant Journal for Cell&Molecular Biology,82,245-255.
Zhao X,Teng W,Li Y,Liu D,Gao G,Li D,Qiu L,Zheng H,Han Y,Li W.2017.Loci and candidate genes conferring resistance to soybean cyst nematode HG type 2.5.7.BMCGenomics,18,462.
Zhou Z,Jiang Y,Wang Z,Gou Z,Lyu J,Li W,Yu Y,Shu L,Zhao Y,Ma Y,Fang C,Shen Y,Liu T,Li C,Li Q,Wu M,Wang M,Wu Y,Dong Y,Wan W,et al.2015.Resequencing302 wild and cultivated accessions identifies genes related to domestication and improvement in soybean.Nature Biotechnology,33,408-414.