| The peduncle vascular system of maize is of critical importance in transportation of photosynthetic products,nutrients,and water to the ear,and has a positive effect on grain yield.However,the genetic basis of PVB-related traits in diverse maize lines remains poorly understood.In this study,with high density SNP markers,the RIL population of Xianyu335 RIL(PH4CV×PH6WC),Zhengdan958(Zheng58×Chang7-2)and an association mapping population were used to dissect the genetic basis of the 15 PVB-related traits.Combined with the comparative transcriptome analysis during the maize peduncle elongation process and candidate gene association analysis,three key candidate genes were identified from key QTL.At the same time,a key candidate gene(Zm VLN2)was further validated using mutants.The main results were as follows:1.There were abundant natural variation of PVB-related traits in maize: Phenotypic statistic of PVB-related traits in two RIL populations and the association mapping population under different locations.The PVB-related traits varied considerably at different locations.Most of the PVB-related traits showed normal distribution,and a few traits showed skew normal distribution,indicating that they were typical quantitative traits and suitable for further study.2.A total of 132 QTL associated with 15 PVB-related traits were identified by linkage analysis: A total of 132 QTL were identified by linkage analysis of 15 PVB-related traits in Yongcheng(YC)and Yuanyang(YY)in 2017.Specifically,29,27 and 25 QTL were identified in the RIL population of Xianyu335 at 17 YC,17YY and the combination of this two locations(BLUP),respectively;31,34 and 33 QTL were identified in the RIL population of Zhengdan958 at the same locations,respectively.9 and 17 co-localized QTL were identified for the RIL populations of Xianyu335 and Zhengdan 958 at different locations,respectively.And 7 co-localized QTL(Co_QTL2,Co_QTL4,Co_QTL7,Co_QTL10,Co_QTL11,Co_QTL13,and Co_QTL14)was identified in the two populations,and they involve the length of ear handle(LEH),the total number of vascular bundles(TNVB),the area of single large vascular bundle(ASLVB),the area of single small vascular bundle(ASSVB),the area of small vascular bundles(ASVB),and the density of vascular bundles(DVB).3.A total of 223 SNPs associated with 15 PVB-related traits were identified by genomewide association study: A set of 0.56 million high quality SNPs were used to perform genome-wide association study(GWAS)on the 15 PVB-related traits,which were obtained from 386 inbred lines.These inbred lines were planted at 17 YC,Kaifeng(KF)and YY in 2020,respectively.At a significant level of P ≤ 3.93 × 10-6,14,88,55 and 66 genetic loci were identified at 17 YC,20KF,20 YY and BLUP(20KF and 20YY),respectively.These SNPs involved 9,41,27 and 28 QTLs,respectively.The phenotypic variation range explained by QTL for these four locations was 8.84% to 11.51%,8.63% to 14.09%,8.74% to 13.21% and 8.34% to 12.11%,respectively.Twenty-one QTL were co-localized in at least two locations.4.Nine co-localize QTL were identified between different populations: In this study,there were 7 co-localized QTL between the RIL population of Xianyu335 and Zhengdan958.q PVB1-11 a and q PVB3-4a in Xianyu335 RIL population were co-located with q PVB12 c and q PVB26 c in association mapping population.This two set of colocalized QTL were associated with the length of ear handle(LEH),the internode number of ear handle(LNEH),the single internode length(SLL),the number of large vascular bundles(NLVB),the number of small vascular bundles(NSVB),the total number of vascular bundles(TNVB),the area of small vascular bundles(ASVB),and the area of large vascular bundles(ALVB),respectively.There was no co-localized QTL between Zhengdan958 RIL population and association mapping population.In addition,q PVB12 c and q PVB1-11 a again overlap with the reported q SL CIK-1-1.q SL CIK-1-1 association with LEH was identified from a CI7/K22 RIL population.These results also indicated the accuracy of the results of this study.5.Three key genes associated with NSVB or LEH were identified by candidate gene association analysis: Based on the functional annotation of the gene,four candidate genes(GRMZM2G045781,GRMZM2G386971,GRMZM2G007404,and GRMZM2G038401)were screened from co-localized QTL(q PVB12 c,q PVB47 c,q PVB56 c,and q PVB61c),respectively.A candidate gene,GRMZM2G028980,was screened from co-localized q PVB4-11 a by combination of linkage analysis and transcriptome sequencing(RNA-seq).In addition,another gene(GRMZM2G180988)was screened from q PVB63 c,which was identified in 17 YC.Candidate gene association analysis revealed showed that GRMZM2G180988 was a key gene affecting NSVB,GRMZM2G028980 and GRMZM2G045781 were both imporeant genes affecting LEH.6.GRMZM2G180988(Zm VLN2)was functional gene in q PVB63c: According to the results of candidate gene association analysis,a B73 EMS mutant(Mut_Sample: EMS4-0afc18)was obtained from maize EMS mutant library.Analysis of variance showed that the P value of NSVB between WT and Zmvln2 was 1.92e-05,which was significant differences at P < 0.001.These results again suggest that GRMZM2G180988(Zmvln2)may be functional genes in q PVB63 c.Haplotype analysis of Zmvln2 showed that NSVB between Hap1 and Hap2 was significant at P < 0.001(P = 3.02e-07).We also checked number of inbred lines according to their temperate and tropical/sub-tropical origins and source of breeding material in the haplotypes.We found that the proportion of tropical/sub-tropical germplasm in Hap1 and Hap2 were 58.66% and 11.36%,Hap2 had majority of China elite maize inbred lines(29/44).These results indicated that Zmvln2 was selected during both domestication and genetic improvement of maize.In conclusion,the results provide important information to enhance understanding of the genetic basis of PVB-related traits and potentially facilitate the breeding of new highyielding maize cultivars. |
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