Genome-wide patterns of genetic variation among elite maize inbred lines

Lai, Jinsheng; Li, Ruiqiang; Xu, Xun; Jin, Weiwei; Xu, Min; Zhao, Hainan; Xiang, Zhongkai; Song, Weibin; Ying, Kai; Zhang, Mei; Jiao, Yinping; Ni, Peixiang; Zhang, Jianguo; Dong, Lü; Guo, Xiaosen; Ye, Kaixiong; Jian, Min; Wang, Bo; Zheng, Huisong; Liang, Huiqing; Zhang, Xiuqing; Wang, Shoucai; Chen, Shaojiang; Li, Jiansheng; Fu, Yan; Springer, Nathan M.; Yang, Huanming; Wang, Jian; Dai, Jingrui; Schnable, Patrick S.; Wang, Jun

doi:10.1038/ng.684

Cited by 441 publications

(396 citation statements)

References 31 publications

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“…After quality control, we identified totally 3,619,762 SNPs using B73 as the reference by a two-step procedure with multiple criteria 11,12 (Table 1). Among them, 2,636,164 SNPs were in the exons, which is 5.6 times greater than that previously reported in a group of six elite maize inbred lines (468,900 exonic SNPs) 13 , 7.5 times higher than that reported in the nested association mapping (NAM) population (352,000 exonic SNPs) 14 and 35.7 times higher than that reported between B73 and Mo17 (73,900 exonic SNPs) 14 . Moreover, 69.7% of SNPs in the NAM population and 87.5% of SNPs in the B73/Mo17 were included in our SNP set (Fig.…”

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confidence: 55%

RNA sequencing reveals the complex regulatory network in the maize kernel

et al. 2013

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RNA sequencing can simultaneously identify exonic polymorphisms and quantitate gene expression. Here we report RNA sequencing of developing maize kernels from 368 inbred lines producing 25.8 billion reads and 3.6 million single-nucleotide polymorphisms. Both the MaizeSNP50 BeadChip and the Sequenom MassArray iPLEX platforms confirm a subset of high-quality SNPs. Of these SNPs, we have mapped 931,484 to gene regions with a mean density of 40.3 SNPs per gene. The genome-wide association study identifies 16,408 expression quantitative trait loci. A two-step approach defines 95.1% of the eQTLs to a 10-kb region, and 67.7% of them include a single gene. The establishment of relationships between eQTLs and their targets reveals a large-scale gene regulatory network, which include the regulation of 31 zein and 16 key kernel genes. These results contribute to our understanding of kernel development and to the improvement of maize yield and nutritional quality.

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confidence: 55%

RNA sequencing reveals the complex regulatory network in the maize kernel

et al. 2013

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“…Taking advantage of recent resequencing results (27), we tested five genes from reciprocal crosses between inbreds Zheng58 and Chang7-2. Our results showed that all of the tested genes had the same imprinting effect in Zheng58 and Chang7-2 as in B73 and Mo17 (SI Appendix, Fig.…”

Section: Resultsmentioning

confidence: 99%

Extensive, clustered parental imprinting of protein-coding and noncoding RNAs in developing maize endosperm

Zhang

Zhao

Xie

et al. 2011

Proc. Natl. Acad. Sci. U.S.A.

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Although genetic imprinting was discovered in maize 40 years ago, its exact extent in the triploid endosperm remains unknown. Here, we have analyzed global patterns of allelic gene expression in developing maize endosperms from reciprocal crosses between inbreds B73 and Mo17. We have defined an imprinted gene as one in which the relative expression of the maternal and paternal alleles differ at least fivefold in both hybrids of the reciprocal crosses. We found that at least 179 genes (1.6% of protein-coding genes) expressed in the endosperm are imprinted, with 68 of them showing maternal preferential expression and 111 paternal preferential expression. Additionally, 38 long noncoding RNAs were imprinted. The latter are transcribed in either sense or antisense orientation from intronic regions of normal protein-coding genes or from intergenic regions. Imprinted genes show a clear pattern of clustering around the genome, with a number of imprinted genes being adjacent to each other. Analysis of allele-specific methylation patterns of imprinted loci in the hybrid endosperm identified 21 differentially methylated regions (DMRs) of several hundred base pairs in length, corresponding to both imprinted genes and noncoding transcripts. All DMRs identified are uniformly hypomethylated in maternal alleles and hypermethylated in paternal alleles, regardless of the imprinting direction of their corresponding loci. Our study indicates highly extensive and complex regulation of genetic imprinting in maize endosperm, a mechanism that can potentially function in the balancing of the gene dosage of this triploid tissue.

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“…Maize, in particular, has a high level of sequence and structural diversity (Buckler et al, 2006;Springer et al, 2009;Lai et al, 2010). A genomic comparison of two maize inbreds, B73 and Mo17, revealed an unprecedented level of genomic structural diversity compared with most higher eukaryotes studied thus far (Springer et al, 2009).…”

Section: Conventional Plant Breeding Sources Of Genetic Variation Usementioning

confidence: 99%

Bringing New Plant Varieties to Market: Plant Breeding and Selection Practices Advance Beneficial Characteristics while Minimizing Unintended Changes

et al. 2017

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Commercial‐scale plant breeding is a complex process in which new crop varieties are continuously being developed to improve yield and agronomic performance over current varieties. A wide array of naturally occurring genetic changes are sources of new characteristics available to plant breeders. During conventional plant breeding, genetic material is exchanged that has the potential to beneficially or adversely affect plant characteristics. For this reason, commercial‐scale breeders have implemented extensive plant selection practices to identify the top‐performing candidates with the desired characteristics while minimizing the advancement of unintended changes. Selection practices in maize (Zea mays L.) breeding involve phenotypic assessments of thousands of candidate lines throughout hundreds of different environmental conditions over many years. Desirable characteristics can also be introduced through genetic modification. For genetically modified (GM) crops, molecular analysis is used to select transformed plants with a single copy of an intact DNA insert and without disruption of endogenous genes. All the while, GM crops go through the same extensive phenotypic characterization as conventionally bred crops. Data from both conventional and GM maize breeding programs are presented to show the similarities between these two processes.

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Genome-wide patterns of genetic variation among elite maize inbred lines

Cited by 441 publications

References 31 publications

RNA sequencing reveals the complex regulatory network in the maize kernel

RNA sequencing reveals the complex regulatory network in the maize kernel

Extensive, clustered parental imprinting of protein-coding and noncoding RNAs in developing maize endosperm

Bringing New Plant Varieties to Market: Plant Breeding and Selection Practices Advance Beneficial Characteristics while Minimizing Unintended Changes

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