| Plant height(PH)and ear height(EH)were very important agronomic traits in the process of maize breeding and production,and they played an important role in lodging-resistance characters also,which affects the yield and quality of maize.So,the genetic analysis of PH,EH and its general combining ability(GCA)in maize at molecular level is of great significance for the genetic improvement of these characters.In previous study,the genotype of 362 maize inbred lines had been detected by the maize SNP50 BeadChip(Contained 56,110 SNP markers)from the American Illumina company.In total of 340 maize inbred lines from these panel were used as experimental materials in this study.The PH and EH of this 340 maize inbred lines were measured by field experiments for more than one year;at the same time,we obtained the test-cross variety followed the top-cross method with the synthetic CZ1302 as the female parent and340 inbred lines as the male parent,then,the GCA effect of PH and EH of the tested inbred lines were determined by the field experiment in many years.In the end,the genome-wide association study was carried out with the data of SNP markers and the results of PH,EH and their GCA effect value.The main results are as follows:1 We obtained 43,979 high-quality and polymorphic SNP markers after filtering all of the markers,the mean distance between adjacent SNPs is 47 kb,and the LD decay distance is about 450-500 kb in all chromosomes.Additionally,the result of the analysis of structure indicated that 340 maize inbred lines should be grouped into three subgroups.The Tropical group was composed of 124 inbred lines,the NSS group consisted of 67 inbred lines,the SS group contained 149 inbred lines,and the representative lines were S37,Ye478 and Qi319,respectively.2 The results of GCA analysis indicated that the GCA effect value of PH and EH of rTropical group was significantly higher than the SS and NSS group,however there was no significant difference between SS and NSS group.In addition,the group of Tropical was more likely to result in the increase of PH and EH,while the SS and NSS subgroug could reduce the PH and EH.The inbred line with the lowest GCA effect value of the PH and EH were Zheng58,Qi205,Zheng29,K22,Zhonghuang64,4866 and 77.On the contrary,the inbred lines with the highest GCA effect value of PH and EH were Y1114、F19、10GY76-111 and CML379,respectively.3 Three significant SNP markers(SNP51894,SNP48752 and SNP12520)associated with PH were detected in different environment,located on 10,9 and 2 chromosomes,and the physical position was 139,995,185 bp,129,403,817 bp and 186,789,026 bp,respectively.2 candidate genes were identified in these markers,GRMZM2G128092 and GRMZM2G001977,respectively.4 Six significant SNP markers associated with EH were searched in different environment.2 of them was SNP25650 and SNP2685,both of the 2 markers located on 5 chromosomes,with the 191,485,086 bp and 184,494,302 bp physical position.SNP27,825 and SNP35,713 markers located on 6 and 9 chromosomes,with the95846377 bp and 12343404 bp physical position.The relatively stable markers,SNP2,008 and SNP2,009,located on 5 chromosomes and could detected in two years,with the 191,361,248 bp and 191,361,140 bp physical position.5 There was only 1 SNP marker associated with the GCA of PH,it’s SNP46795,and located on 10 chromosomes with the 142,181,447 bp physical position.The GRMZM2G025243 gene was detected in this marker.6 Five SNP markers associated with the GCA of EH were identified in different environment.There of them were SNP16224,SNP53029 and SNP53093,located on 3,6 and 1 chromosomes,the physical position were 156,657,291 bp,150,685,172 bp and71,795,509 bp,respectively.Two stable markers were SNP53021 and SNP53024,both of them located on 6 chromosome with the 150,666,399 bp and 150,666,636 bp physical position,respectively.Additionally,GRMZM2G035557,GRMZM2G077662 and GRM7ZM2G:378604 were detected in the 5 significant markers.7 There may have different genetic basis between PH and EH and the GCA of PH and EH. |
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