Comparative population genomics of maize domestication and improvement

Hufford, Matthew B.; Xu, Xun; Heerwaarden, Joost van; Pyhäjärvi, Tanja; Chia, Jer Ming; Cartwright, Reed A.; Elshire, Robert J.; Glaubitz, Jeffrey C.; Guill, Kate; Kaeppler, Shawn M.; Lai, Jinsheng; Morrell, Peter L.; Shannon, Laura M.; Song, Chi; Springer, Nathan M.; Swanson-Wagner, Ruth A.; Tiffin, Peter; Wang, Jun; Zhang, Gengyun; Doebley, John; McMullen, Michael D.; Ware, Doreen; Buckler, Edward S.; Yang, Shuang; Ross‐Ibarra, Jeffrey

doi:10.1038/ng.2309

Cited by 816 publications

(933 citation statements)

References 42 publications

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“…In the soybean landraces and improved cultivars, LD increased to 83 kb and 133 kb, respectively (Fig. 2a), similar to that of cultivated rice (123 kb and 167 kb in indica and japonica, respectively) 18 but much higher than cultivated maize (30 kb) 5 . All three populations had low background LD values, but wild soybean had a relatively higher value (Supplementary Fig.…”

Section: Genomic Variationmentioning

confidence: 53%

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Resequencing 302 wild and cultivated accessions identifies genes related to domestication and improvement in soybean

et al. 2015

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Section: Genomic Variationmentioning

confidence: 53%

“…rufipogon, 20 kb) 17 and wild maize (Z. mays ssp. parviglumis, 22 kb) 5 . In the soybean landraces and improved cultivars, LD increased to 83 kb and 133 kb, respectively (Fig.…”

Section: Genomic Variationmentioning

confidence: 99%

Resequencing 302 wild and cultivated accessions identifies genes related to domestication and improvement in soybean

et al. 2015

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“…3). Although this initial reference enabled rapid progress in maize genomics 1 , the origi nal assembly is composed of more than 100,000 small contigs, many of which are arbitrarily ordered and oriented, markedly complicating detailed analysis of individual loci 6 and impeding investigation of inter genic regions crucial to our understanding of phenotypic variation 7,8 and genome evolution 9,10 .…”

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Improved maize reference genome with single-molecule technologies

Jiao

Peluso

Shi

et al. 2017

Nature

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Complete and accurate reference genomes and annotations provide fundamental tools for characterization of genetic and functional variation 1 . These resources facilitate the determination of biological processes and support translation of research findings into improved and sustainable agricultural technologies. Many reference genomes for crop plants have been generated over the past decade, but these genomes are often fragmented and missing complex repeat regions 2 . Here we report the assembly and annotation of a reference genome of maize, a genetic and agricultural model species, using single-molecule real-time sequencing and high-resolution optical mapping. Relative to the previous reference genome 3 , our assembly features a 52-fold increase in contig length and notable improvements in the assembly of intergenic spaces and centromeres. Characterization of the repetitive portion of the genome revealed more than 130,000 intact transposable elements, allowing us to identify transposable element lineage expansions that are unique to maize. Gene annotations were updated using 111,000 full-length transcripts obtained by single-molecule real-time sequencing 4 . In addition, comparative optical mapping of two other inbred maize lines revealed a prevalence of deletions in regions of low gene density and maize lineage-specific genes.

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“…High levels of sequence similarity are required to map resequencing short reads to a reference genome at the expense of losing information from more diverged genomic regions. Presence-absence variation (PAV) and copy number variation (CNV), which are often associated with agronomic traits 6 , may also be missed 7 . Moreover, a single genome is insufficient to represent the genomic content of a predominantly selfing (autogamous) species, such as G. soja, in which individuals are distinct from one another due to low levels of genetic exchange and recombination 8 .…”

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De novo assembly of soybean wild relatives for pan-genome analysis of diversity and agronomic traits

et al. 2014

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Wild relatives of crops are an important source of genetic diversity for agriculture, but their gene repertoire remains largely unexplored. We report the establishment and analysis of a pan-genome of Glycine soja, the wild relative of cultivated soybean Glycine max, by sequencing and de novo assembly of seven phylogenetically and geographically representative accessions. Intergenomic comparisons identified lineage-specific genes and genes with copy number variation or large-effect mutations, some of which show evidence of positive selection and may contribute to variation of agronomic traits such as biotic resistance, seed composition, flowering and maturity time, organ size and final biomass. Approximately 80% of the pan-genome was present in all seven accessions (core), whereas the rest was dispensable and exhibited greater variation than the core genome, perhaps reflecting a role in adaptation to diverse environments. This work will facilitate the harnessing of untapped genetic diversity from wild soybean for enhancement of elite cultivars.

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Comparative population genomics of maize domestication and improvement

Cited by 816 publications

References 42 publications

Resequencing 302 wild and cultivated accessions identifies genes related to domestication and improvement in soybean

Resequencing 302 wild and cultivated accessions identifies genes related to domestication and improvement in soybean

Improved maize reference genome with single-molecule technologies

De novo assembly of soybean wild relatives for pan-genome analysis of diversity and agronomic traits

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