Genome assembly of a tropical maize inbred line provides insights into structural variation and crop improvement

Yang, Ning; Liu, Jie; Gao, Qiang; Gui, Songtao; Chen, Lu; Yang, L.; Huang, Juan; Deng, Tianquan; Luo, Jingyun; He, Li; Wang, Yuebin; Xu, Pengwei; Peng, Yong; Shi, Zhuoxing; Liu, Lan; Ma, Zeyu; Yang, Xin; Zhang, Qianqian; Bai, Mingzhou; Li, San; Li, Wenqiang; Liu, Lei; Jackson, David; Yan, Jianbing

doi:10.1038/s41588-019-0427-6

Cited by 204 publications

(163 citation statements)

References 64 publications

(78 reference statements)

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“…As the cost of sequencing has been decreased and new omics technologies have arisen, there has been explosive growth in the amount of biological information available for maize. The maize B73 reference genome has recently been updated (1), and four more maize genome assemblies have been released during the last two years (2)(3)(4)(5). The previous two-dimensional genome has recently been resolved in three dimensions with the mapping of open chromatin and the identification of chromatin interactions based on ChiA-PET and Hi-C technologies (6,7).…”

Section: Introductionmentioning

confidence: 99%

“…ZEAMAP includes genome assemblies and annotations of four inbred lines, B73 (1), Mo17 (3), SK (4) and HuangZaoSi (HZS) (5), and a teosinte accession (Zea mays ssp. mexicana) (25), expression patterns of tissues from different development stage of same inbred line (4,9) and same tissue of different samples within the AMP (10), three dimensional chromatin interactions and open chromatins of B73 (6), genetic variations including singlenucleotide polymorphisms (SNPs), small insertions and deletions (InDels) and large structure variations (SVs) generated from the deep sequencing of the AMP and the comparison among reference genome assemblies, the phenotypes and metabolome of the AMP and the related loci mapped by genome-wide association studies (GWAS), expression quantitative trait locus (eQTL)…”

Section: Introductionmentioning

confidence: 99%

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ZEAMAP, a comprehensive database adapted to the maize multi-omics era

Gui

Yang

et al. 2020

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As one of the most extensively cultivated crops, maize (Zea mays L.) has been extensively studied by researchers and breeders for over a century. With advances in high-throughput detection of various omics data, a wealth of multi-dimensional and multi-omics information has been accumulated for maize and its wild relative, teosinte. Integration of this information has the potential to accelerate genetic research and generate improvements in maize agronomic traits. To this end, we constructed ZEAMAP (http://www.zeamap.com), a comprehensive database incorporating multiple reference genomes, annotations, comparative genomics, transcriptomes, open chromatin regions, chromatin interactions, high-quality genetic variants, phenotypes, metabolomics, genetic maps, genetic mapping loci, population structures and domestication selection signals between teosinte and maize. ZEAMAP is user-friendly, with the ability to interactively integrate, visualize and cross-reference multiple different omics datasets. and linkage analysis, the population structure and pedigrees of each germplasm and the selective signals between different teosinte subspecies and maize. ZEAMAP generated comprehensive functional annotations for the annotated gene models in each assembly, and provided useful tools for users to search, analyze and visualize all these different omics data.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

ZEAMAP, a comprehensive database adapted to the maize multi-omics era

Gui

Yang

et al. 2020

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“…Another kernel size gene, ZmSWEET4c , affects kernel weight in a different manner, with its product mediating sugar transport across the basal endosperm transfer cell layer, and shows signals of selection during domestication (Sosso et al, 2015). Recently a further gene, BARELY ANY MERISTEM1d ( ZmBAM1d ) was identified as an additional QTL responsible for kernel weight variation in maize (Yang et al, 2019).…”

Section: Introductionmentioning

confidence: 99%

qKW9encodes a pentatricopeptide repeat protein affecting photosynthesis and grain filling in maize

Huang

Lü

Liu

et al. 2019

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Kernel weight is an important yield component in maize that was selected during domestication. Many kernel weight genes have been identified through mutant analysis, and are mostly involved in the biogenesis and functional maintenance of organelles or other fundamental cellular activities. However, only a limited number of loci underlying quantitative variation in kernel weight have been cloned. Here we characterize a maize kernel weight QTL, qKW9 and find that it encodes a DYW motif pentatricopeptide repeat protein involved in C-to-U editing of NdhB, a subunit of the chloroplast NADH dehydrogenase-like complex. In a null qKW9 background, C-to-U editing of NdhB was abolished, and photosynthesis was reduced, suggesting that qKW9 regulates kernel weight by controling the maternal source of photosynthate for grain filling. Characterization of qKW9 highlights the importance of optimizing photosynthesis on maize grain yield production.

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“…With the further decrease of sequencing price, especially the vigorous development of third generation sequencing technology, new opportunities have been brought for maize functional genomics research. Since the publication of maize B73 reference genome in 2009 (Schnalbe et al 2009), three new maize reference genomes were assembled and released by 2018 and 2019 (Springer et al ; Sun et al ; Yang et al ). Now, Maize GDB contains 12 complete maize genomes and is expected to increase to 40 by 2020.…”

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confidence: 99%