Genetic Analysis And Identification Of QTL Responsible For Ear Row Number And Related Traits In Maize

Maize?Zea mays L.?is one of the most important cereal crops and plays a crucial role in securing the world's food supply.Maize presents better ideal plant type compared with other crops in terms of the structure of the photosynthetic reaction.The growing population exerts great pressure on the achievement of further improvements in grain yield.The inheritance of diversified traits,particularlythose involved in grain yield and its components have been the focus of many studies by different researchers and breeders.As an important yield determinant,the ear row number?ERN?exhibited significantly positive correlation with the grain yield.Compared with other components,the inheritance of ERN exhibited a significant additive effect and is less influenced by situational factors.Therefore,the complex quantitative trait,grain yield of maize,could be dissected into its several related components,and its genetic basis could be preliminarily explained by the effects of QTLs that control it components such as ERN.Firstly,six-generations consisting of P₁,P2,F1,BC1:2,BC2:2 and F2:3 derived from the same cross between inbred B73 and SICAU1212 was used to investigate the inheritance of ERN.SICAU1212?two-ranked with two rows per rank?was derived from silunuo,which was planted in Xishuangbanna,Yunnan Province of China.Notably,Silunuo with many primordial traits was considered as the progenitor of Chinese waxy corn.Compare to modern maize that formed approximately 8-20 rows,SICAU1212 with four rows was the extreme case.The jointed analysis based on the major gene plus poly-gene model of quantitative traits showed that the inheritance of ERN in the cross between B73 and SICAU1212 was controlled by two major genes with additive-dominance and epistatic interaction effects plus poly-gene with additive-dominance and epistatic effects?E-0?.The genetic variance values of major genes in BC1:2,BC2:2 and F2:3 segregations were estimated to 2.8572,8.6022 and 10.6910,while those of poly-gene were 0.3639,0.3713 and 0.7726,respectively.In addition,the heritability values of major gene in the three populations were estimated to 81.06,92.78 and 90.90%,while those of poly-gene were 10.48,4.00 and 6.57%,respectively.Secondly,quantitative trait loci?QTL?for agronomic traits were detected cross two F2 populations,which were derived from a same cross between B73 and SICAU1212,consisting of 233 and 231 individuals,and were developed in Yunnan in 2009 and Sichuan in 2010,respectively.As a result,a total of 33 QTLs were associated with 12 agronomic traits consisting of three plant traits,four ear-related traits and five kernel-related traits.The total phenotypic variation explained by QTL for each trait ranged from 8.60 to 72.67%.Of which,four different QTLs were identified for ERN in the two populations.Each QTL explained from 6.78 to 36.76%of the ERN variation.Notably,three of the 4 QTLs?qERN2-1 at bin 2.02,qERN4-2 at bin 4.08 and qERN8-1 at bin 8.02?were consistently associated with ERN and qERN8-1 simultaneously influenced grain yield,plant diameter,ear diameter and kernel length.In addition,only one significant epistatic interaction was detected among all the 33 QTLs.Previous reports of ERN QTL identified in the region near qERN8-1 in other maize populations were rather sparse,indicating that there might be an unknown QTL or gene for ERN.Thirdly,approximately 2,000 F₂ plants derived from B73-SICAU1212 were used to detect QTL located on chromosome 8.The result revealed that QTL near umc1236 explained 13.98%of phenotypic variance.Meanwhile,another accounting for 13.04%of ERN variance was located at bin 8.04.However,the objective of narrowing down the confidence interval of QTL located at bin 8.02 was not accomplished due to the lack of more efficient molecular markers.In total,753 plants with four rows derived from approximately 3,000 BC1 were employed to narrow down the confidence intervals of QTLs at bin 2.02 and 8.02.Using the insertion/deletion polymorphism markers?Indels??based on the AGI's B73 RefGen_v2 sequence?developed by our laboratory,we found that two QTLs for ERN were located on chr2-11541-bnlg125 and chr8-18233-umc1236,respectively.It was noteworthy that the results agreed with those of our previous studies.Additionally,gene zfl2 was located on bin2.02,whether zfl2 really controls the ERN needs further studies.A population of 325 F6:7 RILs was derived from a cross between inbred B73?many-ranked?and SICAU1212?two-ranked?,which could offer the stable phenotypic and genetic information.The 325 RILs and both parents were planted in three experimental stations located in Yunnan,Sichuan and Neimenggu Provinces of China,during 2012,2013 and 2014,respectively.The 325 RILs were eventually genotyped by 273 markers consisting of 107 SSRs markers and 166 Indels.QTL for the two-ranked versus many-ranked ear?TR?were also detected,which was considered to be one of the five key morphological traits that distinguish maize and teosinte ears.Highly positive phenotypic correlations within ERN-GY were observed,whereas negative phenotypic correlations within ERN-TR and TR-GY during multiple environments.A total of 12,8,1,3,3 and 4 QTLs were associated with ERN,TR,GY,HKW,KL and KW through single-environment mapping,respectively.Each QTL responsible for ERN explained 2.33-21.28%of the phenotypic variation.And the TR variation contributed by individual TR QTL ranged from 2.09 to 12.99%.Notably,only three QTLs,qERN2-1?bin 2.02?,qERN8-1?bin 8.02?and qERN8-2?bin 8.04?,were consistently detected in each environment and by joint analysis among all environments,which simultaneously influenced ERN and TR.One of the three QTL,s,qERN8-1 was also identified as interacting with environment.In addition,nine pairs of significant epistatic interactions?two for ERN and seven for TR?were detected among all identified QTLs.The epistasis between qTR2-1 and qTR8-1 was consistent in most environments.Although several epistasis were detected for the two traits,their effects was all less lower than those of corresponding QTL,indicating that the main effect of significant QTL may have stronger effect on ERN and TR.If one QTL region responsible for certain trait contained or was adjacent to a known mutant gene,which was the only candidate gene affecting the development of this trait,the mutant gene may be regarded as a logical candidate gene.In the present study,one stable QTL?qERN8-1?near 18 Mb simultaneously influenced the ERN and TR.Two mutant genes?vt2 and hifl?mapped to approximately 17 and 22 Mb on chromosome 8 are candidate genes in this region.qERN2-1 at bin 2.02 and qERN4-3 at bin 4.08 havezfl2 and ub3 as flanking marker,respectively.Genes sosl and rel2?were co-localized with two location-specific QTL?qERN4-1 and qERN10-1?,respectively.Further studies are needed to determine whether these candidate genes are the causal genetic variants for these QTL.Controlled crosses between two RILs were made to investigate how a single QTL or different combinations of two and more QTLs influence one phenotype?network?by comparing the phenotype between RIL-Fi and corresponding parental RIL.Although qERN2-1 changed the ERN by 0.21 to 1.33 rows,they did not significantly influence the ERN,which agreed with the finding that decreasing the active copy number of zfl2 can decrease the ERN by approximately one row.qERN4-2,qERN4-3,qERN8-1 and qERN8-2 could change the ERN value of 1.75,0.50,2.57 and 1.06 rows,respectively.Moreover,the results showed that loci on chromosome 8 had an epistatic interaction with loci on chromosome 4,qERN8-1had a synergistic interaction with qERN8-2,and qERN4-2 had an additive interaction with qERN4-3.Remarkably,was located in the marker interval between chr2-zfl2 and chr2-13000,which contained 8 maize genes,there was a high possibility that zfl2 controlled the ERN variance.Therefore,chromosomal regions at bin4.08 and 8.02 were considered as the fine-mapping loci in next study.Two residual heterozygous lines?RHLs-C and Y?derived from the same cross between B73 and RIL315 were utilized to fine-mapping the loci at bin 4.08 and 8.02,respectively.Finally,two regions were located on the marker intervals between chr8-17389 and chr8-18233,chr4-197776 and chr4-ub3,respectively.The former region contained 18 genes,while the latter included 42 genes.This implies gene ub3 might control the ERN variance.Compared with the vascular bundles of B73,Mo 17 and Xiaobalu,those of SICAU1212 presented lest number.One candidate gene,namely chr8-IAA1 identified to be highly homologous with rice and ArabidopsisIAAl,seemed to affect auxin transport and the vascular differentiation.Both the IM size?height and width?had highly significant positive correlations with the ERN,in which variance could explain 85.92 and 92.92%of the ERN variance,respectively,implying the important role of the height and width of IM in determining the ERN.When B73,Mo17 and SICAU1212 were treated with different IAA concentrations,the PH of SICAU1212 was auxin-specific,whereas the IM size of SICAU1212 was inactivated.Whether IAA]presented different molecular mechanisms in diverse organs or tissues of maize,or reduction in IAA1 activity might have a correlation with a decrease in inflorescence meristem size and ERN?...