Genetic Characterization and Linkage Disequilibrium Estimation of a Global Maize Collection Using SNP Markers

Yan, Jianbing; Shah, Trushar; Warburton, Marilyn L.; Buckler, Edward S.; McMullen, Michael D.; Crouch, Jonathan H.

doi:10.1371/journal.pone.0008451

Cited by 355 publications

(373 citation statements)

References 51 publications

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“…Heterogeneous levels of LD were also detected in other plant species, when large sequence data sets were inspected through diverse populations (Flint-Garcia et al, 2003). LD can also be highly variable between chromosomes and between different regions within chromosomes (Yan et al, 2009). Highly heterogeneous levels of LD were also described along the human genome, which could be partially correlated with sequence features (Smith et al, 2005).…”

Section: Ld Patternsmentioning

confidence: 89%

“…Within the same species, wild populations usually harbor lower LD compared with their domesticated counterparts, as shown in barley (Caldwell et al, 2006), soybean (Lam et al, 2010), rice (Zhu et al, 2007), tomato (Arunyawat et al, 2007;Labate et al, 2009) and common bean (Rossi et al, 2009), reflecting changes in effective population size (Mather et al, 2007). In cultivated maize, for which LD was estimated based on large sequence data sets, the mean r 2 was 0.24 over a distance of 100 nucleotides and remained above 0.20 within 2 kb (Yan et al, 2009). Selection during the domestication process is likely the source of extensive LD (Whitt et al, 2002).…”

Section: Ld Patternsmentioning

confidence: 99%

“…For example, genetic diversity parameters have been described at the whole-genome level for Arabidopsis (Nordborg et al, 2005;Kim et al, 2007), maize (Yan et al, 2009); http://www.panzea.org), rice (http://irfgc.irri.org), soybean (Lam et al, 2010) or at the chromosome level for wheat (Horvath et al, 2009). From these surveys of LD, Kim et al (2007) estimated that B140 000 single-nucleotide polymorphisms (SNPs) would be required for the whole scan of the 125-Mb genome of Arabidopsis, whereas Yan et al (2009) estimated this number between 240 000 and 480 000 SNPs for the 2400-Mb genome of maize. A genome-wide analysis showed that LD is so low in grapevine (r 2 o0.20 even between very close sites in Vitis vinifera) that whole-genome sequencing will be required for genome-wide association analyses (Myles et al, 2010).…”

Section: Introductionmentioning

confidence: 99%

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The heterogeneous levels of linkage disequilibrium in white spruce genes and comparative analysis with other conifers

Pavy

Gagnon

et al. 2011

Heredity

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In plants, knowledge about linkage disequilibrium (LD) is relevant for the design of efficient single-nucleotide polymorphism arrays in relation to their use in population and association genomics studies. Previous studies of conifer genes have shown LD to decay rapidly within gene limits, but exceptions have been reported. To evaluate the extent of heterogeneity of LD among conifer genes and its potential causes, we examined LD in 105 genes of white spruce (Picea glauca) by sequencing a panel of 48 haploid megagametophytes from natural populations and further compared it with LD in other conifer species. The average pairwise r 2 value was 0.19 (s.d.¼0.19), and LD dropped quickly with a half-decay being reached at a distance of 65 nucleotides between sites. However, LD was significantly heterogeneous among genes. A first group of 29 genes had stronger LD (mean r 2 ¼0.28), and a second group of 38 genes had weaker LD (mean r 2 ¼0.12). While a strong relationship was found with the recombination rate, there was no obvious relationship between LD and functional classification. The level of nucleotide diversity, which was highly heterogeneous across genes, was also not significantly correlated with LD. A search for selection signatures highlighted significant deviations from the standard neutral model, which could be mostly attributed to recent demographic changes. Little evidence was seen for hitchhiking and clear relationships with LD. When compared among conifer species, on average, levels of LD were similar in genes from white spruce, Norway spruce and Scots pine, whereas loblolly pine and Douglas fir genes exhibited a significantly higher LD.

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Section: Ld Patternsmentioning

confidence: 89%

Section: Ld Patternsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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The heterogeneous levels of linkage disequilibrium in white spruce genes and comparative analysis with other conifers

Pavy

Gagnon

et al. 2011

Heredity

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“…하지만 association mapping은 육종에서의 높은 유용성을 가지고 있음에도 불구하고 일반 연관지도(linkage mapping)에 비해 빈도가 낮은 대립유전자 에서는 활용 가치가 낮은 편이다 (Visscher, 2008 (Gore et al, 2009;Yan et al, 2009 . 염색체의 물리적 거리와 더불어 유전적 부동, 자연 선택, 인공선택, 교배시스템, 다른 집단과의 혼합 등으로 인 하여 LD의 변형(breakdown)에 영향을 준다 (Flint-Garcia, 2003;Yu & Buckler, 2006).…”

Section: Downy Mildew 저항성 육종unclassified

Genetic Improvement of Maize by Marker-Assisted Breeding

Kim¹,

Moon²,

Baek³

et al. 2014

Korean Journal of Crop Science

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Maize is one of the most important food and feed crops in the world including Southeast Asia. In spite of numberous efforts with conventional breeding, the maize productions remain low and the loss of yields by drought and downy mildew are still severe in Asia. Genetic improvement of maize has been performed with molecular marker and genetic engineering. Because maize is one of the most widely studied crop for its own genome and has tremendous diversity and variant, maize is considered as a forefront crop in development and estimation of molecular markers for agricultural useful trait in genetics and breeding. Using QTL (Quantitative Trait Loci) and MAS (Marker Assisted Breeding), molecular breeders are able to accelerate the development of drought tolerance or downy mildew resistance maize genotype. The present paper overviews QTL/MAS approaches towards improvement of maize production against drought and downy mildew. We also discuss here the trends and importance of molecular marker and mapping population in maize breeding.

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“…This transition has already taken place in several major crop species like rice (Nasu et al, 2002), maize (Yan et al, 2009), soybean (Wu et al, 2010), and common bean (Hyten et al, 2010). In case of chickpea, only few hundred ESTs and some reports on identification of SNPs were available until recently.…”

Section: Transcript Sequences and Snp Markersmentioning

confidence: 99%

Genomic tools and germplasm diversity for chickpea improvement

Upadhyaya

Thudi

Dronavalli

et al. 2011

Plant Genet. Resour.

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Chickpea is third most important grain legume grown in the arid and semi-arid regions of the world. In spite of vast germplasm accessions available in different genebanks, there has been very limited use of these accessions in genetic enhancement of chickpea. However, in recent years specialized germplasm sub sets like global composite collection, core collection, mini core collection and reference set have been developed. In parallel, significant genomic resources like molecular markers including simple sequence repeats (SSRs), single nucleotide polymorphsims (SNPs), Diversity Arrays Technologies (DArT) and transcript sequences e.g. expressed sequence tags (ESTs), short transcript reads have been developed. By using SSR, SNP and DArT markers, integrated genetic maps have been developed. It is anticipated that use of genomic resources and specialized germplasm sub sets such as mini core collection and reference set will facilitate identification of trait-specific germplasm, trait mapping and allele mining for resistance to biotic and abiotic stresses and for agronomic traits. Recent advances in genomics and bioinformatics offer the possibility of undertaking large scale sequencing of germplasm accessions so that modern breeding approaches such as genomic selection and breeding by design can be realized in near future for chickpea improvement.

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Genetic Characterization and Linkage Disequilibrium Estimation of a Global Maize Collection Using SNP Markers

Cited by 355 publications

References 51 publications

The heterogeneous levels of linkage disequilibrium in white spruce genes and comparative analysis with other conifers

The heterogeneous levels of linkage disequilibrium in white spruce genes and comparative analysis with other conifers

Genetic Improvement of Maize by Marker-Assisted Breeding

Genomic tools and germplasm diversity for chickpea improvement

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