Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation

Maize HapMap2 Identifies Extant Variation From a Genome in Flux

Jer-Ming Chia et al. Nat Genet.

Abstract

Whereas breeders have exploited diversity in maize for yield improvements, there has been limited progress in using beneficial alleles in undomesticated varieties. Characterizing standing variation in this complex genome has been challenging, with only a small fraction of it described to date. Using a population genetics scoring model, we identified 55 million SNPs in 103 lines across pre-domestication and domesticated Zea mays varieties, including a representative from the sister genus Tripsacum. We find that structural variations are pervasive in the Z. mays genome and are enriched at loci associated with important traits. By investigating the drivers of genome size variation, we find that the larger Tripsacum genome can be explained by transposable element abundance rather than an allopolyploid origin. In contrast, intraspecies genome size variation seems to be controlled by chromosomal knob content. There is tremendous overlap in key gene content in maize and Tripsacum, suggesting that adaptations from Tripsacum (for example, perennialism and frost and drought tolerance) can likely be integrated into maize.

Comment in

Similar articles

See all similar articles

Cited by 225 PubMed Central articles

See all "Cited by" articles

References

    1. Genome Res. 2010 Dec;20(12):1689-99 - PubMed
    1. Bioinformatics. 2009 Aug 1;25(15):1966-7 - PubMed
    1. Bioinformatics. 2010 Jan 1;26(1):139-40 - PubMed
    1. Science. 2010 Jul 2;329(5987):75-8 - PubMed
    1. Science. 2005 May 27;308(5726):1310-4 - PubMed

Publication types

Substances

LinkOut - more resources

Feedback