中国玉米骨干自交系遗传多样性研究
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摘要
玉米(Zea mays L.)是重要的饲料作物、粮食作物和工业原料来源,在国民经济发展中占有举足轻重的地位。与其它作物相比,玉米虽然具有丰富遗传多样性,但是,由于驯化和品种改良等影响,与远古亲缘种墨西哥黍(Zea ssp.Mexicana)相比,具有重要经济价值的基因位点,遗传多样性在不同程度上有所减弱。遗传多样性是植物杂交育种的基础,我国地域广袤,多样性气候条件为我国玉米种质资源向遗传多样化发展提供了广阔空间,培育的自交系是国际育种工作的宝贵资源之一。
本研究采用改进的SNAP(Single Nucleotide Amplified Polymorphism)技术对河南、河北、山东和辽宁等玉米生产大省的67份玉米骨干自交系的遗传多样性进行了研究,检测了参与淀粉合成途径的6个关键基因Bt2、Sh1、Sh2、Wx1、Ae1和Su1的23个SNP位点,参与赤霉素合成途径的3个调节基因d3、An1和D8以及Gl15基因的15个SNP位点,并根据检测结果进行了SNP位点的变异动态分析、单倍型分析、聚类分析和连锁不平衡分析(linkage disequilibrium,LD)。主要研究结果如下:
1.PIC(Polymorphic Information Content)分析结果表明,参与淀粉合成途径的Sh1和Sh2的SNP位点都表现出中度多态性(0.25＜PIC＜0.50);Bt2除有3个中度多态性位点外,还有1个高度多态性位点(PIC≥0.50);Wx1、Ae1和Su1均只有1个中度多态性位点;Bt2、Ae1和Wx1各有1个SNP不具有多态性;Su1有2个SNP不具多态性。参与赤霉素代谢调节的3个基因位点D8、d3和An1多态性较低或没有多态性,其中,D8具1个高度多态和1个中度多态性SNP,其他5个SNP和d3-1986位点均具低多态性,An1的2个SNP位点和d3的另3个SNP位点没有多态性。
2.单倍型数目均比预期数少。参与淀粉合成途径的6个基因的,单倍型数目按减少程度由低到高的次序,分别为Sh2、Sh1、Wx1、Ae1、Su1和Bt2;每个单倍型的种质数目有差异,如Bt2有13个单倍型,其中4个ACAGCA、ACCGCA、ATCGAG和GTCGAG是主要的单倍型,67份种质中分别占23、7、18和5份,前两个单倍型种质籽粒均为(偏)硬粒型,后两个单倍型种质籽粒均为(半)马齿型。单倍型多样性分析结果还表明,参与赤霉素代谢调节的3个基因的单倍型数目减少严重,D8的7个SNP位点仅有20个单倍型。
3.根据参与淀粉合成途径6个基因的23个SNP标记结果,67份种质可分为两大类群Ⅰ和Ⅱ;Ⅰ类群有36个品种,包括34个(偏)硬粒品种,Ⅱ类群有31个品种,包括28个(半)马齿型品种;Bt2的2个SNP位点Bt2-2和Bt2-5是两个表型串的分支点,CC和TA是两个SNP位点的主要单倍型,Ⅰ类群有30个(偏)硬粒品种是单倍型CC,单倍型TA的种质全部是(半)马齿型品种且仅分布在类群Ⅱ;两个表型串Ⅰ和Ⅱ各又分为5个不同的亚群,其中,亚群Ⅰ-Ⅱ和Ⅰ-Ⅲ分别以黄早四改良系(7/13)和美国杂交种78599选育系为主(4/5),而12份瑞德黄马牙种质分散在6个不同的亚群。此外,根据参与赤霉素代谢调节的3个基因的SNP标记结果,67份种质也可分为两个类群,第一类群包括5个亚群:Ⅰ-Ⅰ亚群以花期适中硬粒型品系为主,Ⅰ-Ⅱ亚群分为早花硬粒型a类种质和以花期适中(半)马齿型种质为主的b类,Ⅰ-Ⅲ亚群以花期各不同的(偏)硬粒型品系为主,Ⅰ-Ⅳ亚群以花期适中(半)马齿型品系为主,Ⅰ-Ⅴ亚群分为以花期适中(半)马齿型为主的a类和以晚花型品系为主b类。Ⅰ-Ⅰ、Ⅰ-Ⅱ和Ⅰ-Ⅲ亚群以温带种质为主,Ⅰ-Ⅳ和Ⅰ-Ⅴ亚群以(亚)热带种质为主;第二类群仅有自330一份种质。尽管选用的标记不同,但某些玉米品系,如B73、S73、9046和K12S22在两种分类结果中,均在同一亚群。
4.Bt2的Bt2-1、Bt2-2、Bt2-3、Bt2-5利Bt2-6基因内显著连锁不平衡(除Bt2-1和Bt2-3之间),Sh1-2与Sh1-3之间和Sh1-4与Sh1-5之间显著性连锁不平衡;与(偏)硬粒型亚群相比,(半)马齿型亚群的Bt2-2与Bt2-5位点基因内显著连锁不平衡。除D8-1966利Gl15-2829之间外,参与赤霉素合成途径的调节基因d3、An1和D8及Gl15等4个基因其他SNP位点间没有显著连锁不平衡。
Maize(Zea May) is one of the most agronomically important cereal crops in the world.Corn is important not only for food and feed,but also for raw material for a variety of industries.Maize is one of the most molecular diversity grasses.However,genetic variation of some agronomically important pathways may have been reduced in contrast to its closest wild relative,teosinte(Zea ssp.Mexicana) due to demonstation and breeding procedures.The genetic diversity is the foundation of plant breeding.China is a country with a vast territory and diverse climate,which is propitious to develop phenotypical and genetic diversity of maize.These maize lines are valuable resources for future maize breeding.
In this paper,using the modified SNAP method we studied the genetic diversity of 67 germplasm lines,representing a broad cross section of breeding germplasms in China,collected from Liaoning, Guangxi,Henan,Hubei,Shandong Shanxi and Henan provinces.Two agronomically important pathways were involved.One was starch pathway.Another was Gibberellins(GAs) biosynthesis pathway.We measured 38 SNPs distributiong in 10 genes,and determined the dynamics of variation SNP sites,haplotype,across the lines.Clustering and linkage disequilibrium of SNPs were also discussed.The results are summarized as followings.
1.All measured SNPs in Sh1 and Sh2 showed medium polymorphism,where PIC value was between 0.25 and 0.50.Three SNPs at Bt2 locus showed medium polymorphism and one showed high polymorphism,where PIC value was 0.50.Only one SNP in each Wx1,Ae1 and Su1,showed medium polymorphism.One SNP in each Bt2,Wx1 and Ae1,showed no polymorphism,where PIC value was zero.Two SNPs at Su1 locus showed no polymorphism as well.In addition,the value of PIC showed that SNPs of three genes associated with GAs synthesis had low or no polymorphism.D8 had one high and one medium polymorphic site.The rest of five sites of D8 and d3-1986 showed low polymorphism.The measured SNPs of An1 and three ones of d3 showed no polymorphism.
2.The haplotypes were less than the predicated number of 2~n.The reduction extent from high to low was Bt2,Su1,Ae1,Wx1,Sh1 and Sh2,which genes were accossicated with starch synthesis.With 6 SNPs measured for Bt2,13 haplotypes were observed vs.64 haplotypes predicted(2~6).Out of the 13 haplotypes,4 haplotypes,ACAGCA,ACCGCA,ATCGAG and GTCGAG,were most frequently presented in the analyzed lines.There were 23 and 7 lines corresponding to the haplotypes ACAGCA and ACCGCA,respectively.More interestingly,all these 30 lines had the same(semi-) flint phenotype.There were 18 and 5 lines corresponding to the haplotypes ATCGAG and GTCGAG, respectively,and these 23 lines had the same(semi-) dent phenotype.Based on the results of seven SNPs,D8 only had 20 haplotypes and showed low diversity.
3.Sixty-seven lines were clustered into two groups based on the SNAP results of 6 starch synthesis genes.GroupⅠincluded 34(semi-) flint lines and groupⅡincluded 28(semi-) dent ones. Out of the 34(semi-) flint lines of groupⅠ,31 lines in grouplhad had the commone haplotype of CC at Bt2 locus(Bt2-2 and Bt2-5),while 25(semi-) dent lines out of groupⅡhad haplotype of TA.Each group was divided into five subgroups.Most lines in GroupⅠ-ⅡandⅠ-Ⅲwere relatives or offsprings of Huangzao4 and of an American hybrid lines 78599,respetctively.Twenve relatives or offsprings of Reid were clustered into 6 subgroups.Base on the SNAP results of D8,An1,d3 and Gl15,sixty-seven lines were also clustered into two groups.GroupⅡonly had one line,Zi330.GroupⅠwas divided into five subgroups.Most lines in subgroupⅠ-Ⅰwere flint lines with medium flowering time.SubgroupⅠ-Ⅱhad 2 typical phenotypes:a) flint with early flowering time b)(semi) dent with medium flowering time.Most of lines in subgroupⅠ-Ⅲwere(semi) flint with different flowering time.Most of lines in subgroupⅠ-Ⅳwere(semi) dent with medium flowering time.SubgroupⅠ-Ⅴwas divided into two types based on their phenotypes:a)(semi) dent with medium flowering time b) late flowering time with different kernel phenotype.Most of lines in subgroupsⅠ-Ⅰ,Ⅰ-ⅡandⅠ-Ⅲwere temperature origin. Most of lines in subgroupsⅠ-ⅣandⅠ-Ⅴwere(sub) tropical origin.Though the SNAPs available were different,some lines such as B73,S73,9046 and K12S22 were all in the same subgroups in both clustering results.
4.SNPs in Bt2,Sh1 and Ae1 showed significant intragenic LD and in Bt2,Sh1 and Su1 showed intergenic LD.Except between Bt2-1 and Bt2-3,all other pairs of 5 SNPs in Bt2(Bt2-1,Bt2-2,Bt2-3, Bt2-5,Bt2-6) showed significant intragenic LD.In Sh1,two pairs(Sh1-2 and Sh1-3,Sh1-4 and Sh1-5) showed significant intragenic LD.The pairs of Bt2-2 and Bt2-5 only showed significant LD in(semi-) dent population.There was no significant LD except one pair,D8-1966 and Gl15-2829,in D8,An1, d3 and Gl15.
本研究采用改进的SNAP(Single Nucleotide Amplified Polymorphism)技术对河南、河北、山东和辽宁等玉米生产大省的67份玉米骨干自交系的遗传多样性进行了研究,检测了参与淀粉合成途径的6个关键基因Bt2、Sh1、Sh2、Wx1、Ae1和Su1的23个SNP位点,参与赤霉素合成途径的3个调节基因d3、An1和D8以及Gl15基因的15个SNP位点,并根据检测结果进行了SNP位点的变异动态分析、单倍型分析、聚类分析和连锁不平衡分析(linkage disequilibrium,LD)。主要研究结果如下:
1.PIC(Polymorphic Information Content)分析结果表明,参与淀粉合成途径的Sh1和Sh2的SNP位点都表现出中度多态性(0.25＜PIC＜0.50);Bt2除有3个中度多态性位点外,还有1个高度多态性位点(PIC≥0.50);Wx1、Ae1和Su1均只有1个中度多态性位点;Bt2、Ae1和Wx1各有1个SNP不具有多态性;Su1有2个SNP不具多态性。参与赤霉素代谢调节的3个基因位点D8、d3和An1多态性较低或没有多态性,其中,D8具1个高度多态和1个中度多态性SNP,其他5个SNP和d3-1986位点均具低多态性,An1的2个SNP位点和d3的另3个SNP位点没有多态性。
2.单倍型数目均比预期数少。参与淀粉合成途径的6个基因的,单倍型数目按减少程度由低到高的次序,分别为Sh2、Sh1、Wx1、Ae1、Su1和Bt2;每个单倍型的种质数目有差异,如Bt2有13个单倍型,其中4个ACAGCA、ACCGCA、ATCGAG和GTCGAG是主要的单倍型,67份种质中分别占23、7、18和5份,前两个单倍型种质籽粒均为(偏)硬粒型,后两个单倍型种质籽粒均为(半)马齿型。单倍型多样性分析结果还表明,参与赤霉素代谢调节的3个基因的单倍型数目减少严重,D8的7个SNP位点仅有20个单倍型。
3.根据参与淀粉合成途径6个基因的23个SNP标记结果,67份种质可分为两大类群Ⅰ和Ⅱ;Ⅰ类群有36个品种,包括34个(偏)硬粒品种,Ⅱ类群有31个品种,包括28个(半)马齿型品种;Bt2的2个SNP位点Bt2-2和Bt2-5是两个表型串的分支点,CC和TA是两个SNP位点的主要单倍型,Ⅰ类群有30个(偏)硬粒品种是单倍型CC,单倍型TA的种质全部是(半)马齿型品种且仅分布在类群Ⅱ;两个表型串Ⅰ和Ⅱ各又分为5个不同的亚群,其中,亚群Ⅰ-Ⅱ和Ⅰ-Ⅲ分别以黄早四改良系(7/13)和美国杂交种78599选育系为主(4/5),而12份瑞德黄马牙种质分散在6个不同的亚群。此外,根据参与赤霉素代谢调节的3个基因的SNP标记结果,67份种质也可分为两个类群,第一类群包括5个亚群:Ⅰ-Ⅰ亚群以花期适中硬粒型品系为主,Ⅰ-Ⅱ亚群分为早花硬粒型a类种质和以花期适中(半)马齿型种质为主的b类,Ⅰ-Ⅲ亚群以花期各不同的(偏)硬粒型品系为主,Ⅰ-Ⅳ亚群以花期适中(半)马齿型品系为主,Ⅰ-Ⅴ亚群分为以花期适中(半)马齿型为主的a类和以晚花型品系为主b类。Ⅰ-Ⅰ、Ⅰ-Ⅱ和Ⅰ-Ⅲ亚群以温带种质为主,Ⅰ-Ⅳ和Ⅰ-Ⅴ亚群以(亚)热带种质为主;第二类群仅有自330一份种质。尽管选用的标记不同,但某些玉米品系,如B73、S73、9046和K12S22在两种分类结果中,均在同一亚群。
4.Bt2的Bt2-1、Bt2-2、Bt2-3、Bt2-5利Bt2-6基因内显著连锁不平衡(除Bt2-1和Bt2-3之间),Sh1-2与Sh1-3之间和Sh1-4与Sh1-5之间显著性连锁不平衡;与(偏)硬粒型亚群相比,(半)马齿型亚群的Bt2-2与Bt2-5位点基因内显著连锁不平衡。除D8-1966利Gl15-2829之间外,参与赤霉素合成途径的调节基因d3、An1和D8及Gl15等4个基因其他SNP位点间没有显著连锁不平衡。
Maize(Zea May) is one of the most agronomically important cereal crops in the world.Corn is important not only for food and feed,but also for raw material for a variety of industries.Maize is one of the most molecular diversity grasses.However,genetic variation of some agronomically important pathways may have been reduced in contrast to its closest wild relative,teosinte(Zea ssp.Mexicana) due to demonstation and breeding procedures.The genetic diversity is the foundation of plant breeding.China is a country with a vast territory and diverse climate,which is propitious to develop phenotypical and genetic diversity of maize.These maize lines are valuable resources for future maize breeding.
In this paper,using the modified SNAP method we studied the genetic diversity of 67 germplasm lines,representing a broad cross section of breeding germplasms in China,collected from Liaoning, Guangxi,Henan,Hubei,Shandong Shanxi and Henan provinces.Two agronomically important pathways were involved.One was starch pathway.Another was Gibberellins(GAs) biosynthesis pathway.We measured 38 SNPs distributiong in 10 genes,and determined the dynamics of variation SNP sites,haplotype,across the lines.Clustering and linkage disequilibrium of SNPs were also discussed.The results are summarized as followings.
1.All measured SNPs in Sh1 and Sh2 showed medium polymorphism,where PIC value was between 0.25 and 0.50.Three SNPs at Bt2 locus showed medium polymorphism and one showed high polymorphism,where PIC value was 0.50.Only one SNP in each Wx1,Ae1 and Su1,showed medium polymorphism.One SNP in each Bt2,Wx1 and Ae1,showed no polymorphism,where PIC value was zero.Two SNPs at Su1 locus showed no polymorphism as well.In addition,the value of PIC showed that SNPs of three genes associated with GAs synthesis had low or no polymorphism.D8 had one high and one medium polymorphic site.The rest of five sites of D8 and d3-1986 showed low polymorphism.The measured SNPs of An1 and three ones of d3 showed no polymorphism.
2.The haplotypes were less than the predicated number of 2~n.The reduction extent from high to low was Bt2,Su1,Ae1,Wx1,Sh1 and Sh2,which genes were accossicated with starch synthesis.With 6 SNPs measured for Bt2,13 haplotypes were observed vs.64 haplotypes predicted(2~6).Out of the 13 haplotypes,4 haplotypes,ACAGCA,ACCGCA,ATCGAG and GTCGAG,were most frequently presented in the analyzed lines.There were 23 and 7 lines corresponding to the haplotypes ACAGCA and ACCGCA,respectively.More interestingly,all these 30 lines had the same(semi-) flint phenotype.There were 18 and 5 lines corresponding to the haplotypes ATCGAG and GTCGAG, respectively,and these 23 lines had the same(semi-) dent phenotype.Based on the results of seven SNPs,D8 only had 20 haplotypes and showed low diversity.
3.Sixty-seven lines were clustered into two groups based on the SNAP results of 6 starch synthesis genes.GroupⅠincluded 34(semi-) flint lines and groupⅡincluded 28(semi-) dent ones. Out of the 34(semi-) flint lines of groupⅠ,31 lines in grouplhad had the commone haplotype of CC at Bt2 locus(Bt2-2 and Bt2-5),while 25(semi-) dent lines out of groupⅡhad haplotype of TA.Each group was divided into five subgroups.Most lines in GroupⅠ-ⅡandⅠ-Ⅲwere relatives or offsprings of Huangzao4 and of an American hybrid lines 78599,respetctively.Twenve relatives or offsprings of Reid were clustered into 6 subgroups.Base on the SNAP results of D8,An1,d3 and Gl15,sixty-seven lines were also clustered into two groups.GroupⅡonly had one line,Zi330.GroupⅠwas divided into five subgroups.Most lines in subgroupⅠ-Ⅰwere flint lines with medium flowering time.SubgroupⅠ-Ⅱhad 2 typical phenotypes:a) flint with early flowering time b)(semi) dent with medium flowering time.Most of lines in subgroupⅠ-Ⅲwere(semi) flint with different flowering time.Most of lines in subgroupⅠ-Ⅳwere(semi) dent with medium flowering time.SubgroupⅠ-Ⅴwas divided into two types based on their phenotypes:a)(semi) dent with medium flowering time b) late flowering time with different kernel phenotype.Most of lines in subgroupsⅠ-Ⅰ,Ⅰ-ⅡandⅠ-Ⅲwere temperature origin. Most of lines in subgroupsⅠ-ⅣandⅠ-Ⅴwere(sub) tropical origin.Though the SNAPs available were different,some lines such as B73,S73,9046 and K12S22 were all in the same subgroups in both clustering results.
4.SNPs in Bt2,Sh1 and Ae1 showed significant intragenic LD and in Bt2,Sh1 and Su1 showed intergenic LD.Except between Bt2-1 and Bt2-3,all other pairs of 5 SNPs in Bt2(Bt2-1,Bt2-2,Bt2-3, Bt2-5,Bt2-6) showed significant intragenic LD.In Sh1,two pairs(Sh1-2 and Sh1-3,Sh1-4 and Sh1-5) showed significant intragenic LD.The pairs of Bt2-2 and Bt2-5 only showed significant LD in(semi-) dent population.There was no significant LD except one pair,D8-1966 and Gl15-2829,in D8,An1, d3 and Gl15.
引文
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