Association Mapping for Enhancing Maize (<i>Zea mays</i> L.) Genetic Improvement

Yan, Jianbing; Warburton, Marilyn L.; Crouch, Jonathan H.

doi:10.2135/cropsci2010.04.0233

Cited by 309 publications

(244 citation statements)

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“…Maize shows an amazing degree of phenotypic variation due to the outcrossing nature, and to natural and artificial selection during the rapid worldwide population expansion (Yan et al 2011). Phenotypic variation has been explored by QTL mapping and genome-wide association studies (GWAS; Huang and Han 2014).…”

Section: Introductionmentioning

confidence: 99%

Maize pan-transcriptome provides novel insights into genome complexity and quantitative trait variation

Jin

Liu

et al. 2015

Preprint

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Variation in gene expression contributes to the diversity of phenotype. The construction of the pan-transcriptome is especially necessary for species with complex genomes, such as maize. However, knowledge of the regulation mechanisms and functional consequences of the pan-transcriptome is limited. In this study, we identified 13,382 nuclear expression presence and absence variation candidates (ePAVs, expressed in 5%~95% lines; based on the reference genome) by re-analyzing the RNA sequencing data from the kernels (15 days after pollination) of 368 maize diverse inbreds. It was estimated that only ~1% of the ePAVs are explained by DNA sequence presence and absence variations (PAV). The ePAV genes tend to be regulated by distant eQTLs when compared with non-ePAV genes (called here core expression genes, expressed in more than 95% lines). When the expression presence/absence status was used as the "genotype" to perform genome-wide association study, 56 (0.42%) ePAVs were significantly associated with 15 agronomic traits and 1,967 (14.74%) with 526 metabolic traits, measured from the mature kernels. While the above was majorly based on the reference genome, by using a modified 'assemble-then-align' strategy, 2,355 high confidence novel sequences with a total length of 1.9Mb were found absent in the current B73 reference genome (v2). Ten randomly selected novel sequences were validated with genomic PCR. A simulation analysis suggested that the pan-transcriptome of the maize whole kernel is approaching a maximum value of 63,000 genes. Two novel validated sequences annotated as NBS_LRR like genes were found to associate with flavonoid content and their homologs in rice were also found to affect flavonoids and disease-resistance. Novel sequences absent in the present reference genome might be functionally important and deserve more attentions. This study provides novel perspectives and resources to discover maize quantitative trait variations and help us to better understand the kernel regulation networks, thus enhancing maize breeding.

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Section: Introductionmentioning

confidence: 99%

Maize pan-transcriptome provides novel insights into genome complexity and quantitative trait variation

Jin

Liu

et al. 2015

Preprint

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“…Again, these variants could have existed in the wild ancestor and passed through the domestication bottleneck due to small selection coefficients, or they may represent new variation that arose from mutation following domestication. To test these hypotheses, phenotypic evaluations of domestication-related traits and genotypic data of two diverse maize populations were combined in this study to facilitate estimation of the proportion of variation due to polygenic, small-effect QTL vs. larger-effect variants and to compare the genomic positions of larger-effect variants to the known locations of domestication genes.Numerous association mapping panels are already available in maize (Yan et al 2011). The largest and most diverse population that is publicly available is a set of 2815 inbred lines maintained by the U.S. Department of Agriculture North Central Region Plant Introduction Station (NCRPIS) (Romay et al 2013).…”

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confidence: 99%

“…Numerous association mapping panels are already available in maize (Yan et al 2011). The largest and most diverse population that is publicly available is a set of 2815 inbred lines maintained by the U.S. Department of Agriculture North Central Region Plant Introduction Station (NCRPIS) (Romay et al 2013).…”

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confidence: 99%

Genetic Architecture of Domestication-Related Traits in Maize

et al. 2016

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Strong directional selection occurred during the domestication of maize from its wild ancestor teosinte, reducing its genetic diversity, particularly at genes controlling domestication-related traits. Nevertheless, variability for some domestication-related traits is maintained in maize. The genetic basis of this could be sequence variation at the same key genes controlling maize-teosinte differentiation (due to lack of fixation or arising as new mutations after domestication), distinct loci with large effects, or polygenic background variation. Previous studies permit annotation of maize genome regions associated with the major differences between maize and teosinte or that exhibit population genetic signals of selection during either domestication or postdomestication improvement. Genome-wide association studies and genetic variance partitioning analyses were performed in two diverse maize inbred line panels to compare the phenotypic effects and variances of sequence polymorphisms in regions involved in domestication and improvement to the rest of the genome. Additive polygenic models explained most of the genotypic variation for domesticationrelated traits; no large-effect loci were detected for any trait. Most trait variance was associated with background genomic regions lacking previous evidence for involvement in domestication. Improvement sweep regions were associated with more trait variation than expected based on the proportion of the genome they represent. Selection during domestication eliminated large-effect genetic variants that would revert maize toward a teosinte type. Small-effect polygenic variants (enriched in the improvement sweep regions of the genome) are responsible for most of the standing variation for domestication-related traits in maize.KEYWORDS quantitative trait loci; nested association mapping; genome-wide association study; variance components; Zea mays T HE domestication of all major crop plants occurred in a relatively short period in human history, starting 10,000 years ago (Harlan 1992). During the domestication process, seeds of preferred forms were selected and saved to plant subsequent generations. Some alleles favored under domestication may have been neutral or even deleterious for the survival of wild plant species; for example, seed shattering promotes seed dispersal in wild grasses, but alleles for nondisarticulating seed structures were strongly selected for under domestication (Galinat 1983). Consequently, rare alleles favorable for growth and development under agricultural conditions or for traits desired by humans increased in frequency, often reaching fixation and reducing genetic variation very near causal sequence sites (Wang et al. 1999). In addition, domestication was often accompanied by severe genetic bottlenecks from the use of small founder populations. The reduction in effective population sizes also resulted in reduced genetic diversity genome-wide. Population genetics methods to model the strength and duration of bottlenecks provide a means to ...

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“…The results indicated that choice of the core collection could maximize the number of historical recombinations and mutation events and thus reduce LD within and around the gene of interest which is critical for the success of association analysis (Yan et al, 2011). Such short LD decay distance suggested that fine mapping with a core collection for desirable genes could be possible.…”

Section: Population Structure and Ld Patternmentioning

confidence: 99%

“…Furthermore, choice of an appropriate germplasm to maximize the genetic diversity and the number of historical recombinations and mutation events (and thus reduce LD) within and around the gene of interest is critical for the success of association analysis (Yan et al, 2011). As described above, core collections are the core subset of the original collections with minimum samples while having the maximum genetic variability contained within the gene pool.…”

Section: Association Mapping With the Rice Core Collectionmentioning

confidence: 99%