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TeoNAM: A Nested Association Mapping Population for Domestication and Agronomic Trait Analysis in Maize.

Recombinant inbred lines (RILs) are an important resource for mapping genes controlling complex traits in many species. While RIL populations have been developed for maize, a maize RIL population with multiple teosinte inbred lines as parents has been lacking. Here, we report a teosinte nested association mapping population (TeoNAM), derived from crossing five teosinte inbreds to the maize inbred line W22.

Chen QYang CJYork AMXue WDaskalska LLDeValk CAKrueger KWLawton SBSpiegelberg BGSchnell JMNeumeyer MAPerry JSPeterson ACKim BBergstrom LYang LBarber ICTian FDoebley JF.

 

Genetics. 2019 Sep 3. pii: genetics.302594.2019. doi: 10.1534/genetics.119.302594. [Epub ahead of print]

Abstract

Recombinant inbred lines (RILs) are an important resource for mapping genes controlling complex traits in many species. While RIL populations have been developed for maize, a maize RIL population with multiple teosinte inbred lines as parents has been lacking. Here, we report a teosinte nested association mapping population (TeoNAM), derived from crossing five teosinte inbreds to the maize inbred line W22. The resulting 1257 BC1S4 RILs were genotyped with 51,544 SNPs, providing a high-density genetic map with a length of 1540 cM. On average, each RIL is 15% homozygous teosinte and 8% heterozygous. We performed joint linkage mapping (JLM) and genome-wide association study (GWAS) for 22 domestication and agronomic traits. A total of 255 QTLs from JLM were identified with many of these mapping near known genes or novel candidate genes. TeoNAM is a useful resource for QTL mapping for the discovery of novel allelic variation from teosinte. TeoNAM provides the first report that PROSTRATE GROWTH1, a rice domestication gene, is also a QTL associated with tillering in teosinte and maize. We detected multiple QTLs for flowering time and other traits for which the teosinte allele contributes to a more maize-like phenotype. Such QTL could be valuable in maize improvement.

 

See https://www.genetics.org/content/genetics/early/2019/09/03/genetics.119.302594.full.pdf

 

Figure 1: Genomic distribution of QTLs for all 22 traits in TeoNAM. The 22 agronomic (A) and domestication (B) traits are plotted in layers with different background colors, following the order of ASI, BARE, DTA, DTS, PLHT, TBN, YEPE, CULM, EB, ED, EL, GLCO, GLUM, KRN, KW, LFLN, LFWD, PROL, REPE, SHN, STAM and TILN outwards. Black dots indicate QTL peaks detected by JLM and colored bars indicate the support interval of QTLs for different traits. The heat map in the outmost layer (C) shows the number of QTL peaks using a sliding window of 10 cM and 1 cM steps, where low to high density of QTLs (0-12) are shown in light to dark red, respectively.

 


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