The Study On The Genetic Diversity Of Chinese Elite Corns

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.Groupâ… included 34(semi-) flint lines and groupâ…¡included 28(semi-) dent ones. Out of the 34(semi-) flint lines of groupâ… ,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 groupâ…¡had haplotype of TA.Each group was divided into five subgroups.Most lines in Groupâ… -â…¡andâ… -â…¢were 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.Groupâ…¡only had one line,Zi330.Groupâ… was divided into five subgroups.Most lines in subgroupâ… -â… were flint lines with medium flowering time.Subgroupâ… -â…¡had 2 typical phenotypes:a) flint with early flowering time b)(semi) dent with medium flowering time.Most of lines in subgroupâ… -â…¢were(semi) flint with different flowering time.Most of lines in subgroupâ… -â…£were(semi) dent with medium flowering time.Subgroupâ… -â…¤was 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 subgroupsâ… -â… ,â… -â…¡andâ… -â…¢were temperature origin. Most of lines in subgroupsâ… -â…£andâ… -â…¤were(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.