Status and Prospects of Association Mapping in Plants

Zhu, Chengsong; Gore, Michael A.; Buckler, Edward S.; Yu, Jianming

doi:10.3835/plantgenome2008.02.0089

Cited by 1,099 publications

(886 citation statements)

References 163 publications

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“…In contrast to QTL mapping based on bi-parental populations, GWAS uses a sample of lines from the broader breeding population, unrelated by any specific crossing design (Zhu et al 2008). In such studies, associations between genotype and phenotype depend on historical LD broken down by many generations of recombination.…”

Section: Introductionmentioning

confidence: 99%

Genome-wide association study for oat (Avena sativa L.) beta-glucan concentration using germplasm of worldwide origin

et al. 2012

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Detection of quantitative trait loci (QTL) controlling complex traits followed by selection has become a common approach for selection in crop plants. The QTL are most often identified by linkage mapping using experimental F2, backcross, advanced inbred, or doubled haploid families. An alternative approach for QTL detection are genome-wide association studies (GWAS) that use pre-existing lines such as those found in breeding programs. We explored the implementation of GWAS in oat (Avena sativa L.) to identify QTL affecting β-glucan concentration, a soluble dietary fiber with several human health benefits when consumed as a whole grain. A total of 431 lines of worldwide origin were tested over 2 years and genotyped using Diversity Array Technology (DArT) markers. A mixed model approach was used where both population structure fixed effects and pair-wise kinship random effects were included. Various mixed models that differed with respect to population structure and kinship were tested for their ability to control for false positives. As expected, given the level of population structure previously described in oat, population structure did not play a large role in controlling for false positives. Three independent markers were significantly associated with β-glucan concentration. Significant marker sequences were compared with rice and one of the three showed sequence homology to genes localized on rice chromosome seven adjacent to the CslFgene family, known to have β-glucan synthase function. Results indicate that GWAS in oat can be a successful option for QTL detection, more so with future development of higher-density markers. Abstract Detection of quantitative trait loci (QTL) controlling complex traits followed by selection has become a common approach for selection in crop plants. The QTL are most often identified by linkage mapping using experimental F 2 , backcross, advanced inbred, or doubled haploid families. An alternative approach for QTL detection are genome-wide association studies (GWAS) that use pre-existing lines such as those found in breeding programs. We explored the implementation of GWAS in oat (Avena sativa L.) to identify QTL affecting b-glucan concentration, a soluble dietary fiber with several human health benefits when consumed as a whole grain. A total of 431 lines of worldwide origin were tested over 2 years and genotyped using Diversity Array Technology (DArT) markers. A mixed model approach was used where both population structure fixed effects and pair-wise kinship random effects were included. Various mixed models that differed with respect to population structure and kinship were tested for their ability to control for false positives. As expected, given the level of population structure previously described in oat, population structure did not play a large role in controlling for false positives. Three independent markers were significantly associated with b-glucan concentration. Significant marker sequences were compared with rice and one of the three showed sequence hom...

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Section: Introductionmentioning

confidence: 99%

Genome-wide association study for oat (Avena sativa L.) beta-glucan concentration using germplasm of worldwide origin

et al. 2012

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“…특히 연관지도(association mapping) 은 새로운 유전자나 혹은 관련될 것으로 예측하는 유전자의 검정을 위하여 매우 유용하고 효율적인 방법으로 이용되고 있다 (Altshuler et al, 2008;Hunter and Crawford, 2008). 특히 식물에서는 동물보다 더 유용성이 뛰어나기 때문에 작 물 육종 분야에서 활용도가 점차 증가하고 있는 추세이다 (Zhu et al, 2008). 일반적인 유전자 연관지도(linkage mapping)…”

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 results in a relatively low mapping resolution (Flint-Garcia et al, 2003). By contrast, for association mapping, historical recombination and natural genetic diversity of the different populations lead to a higher mapping resolution (Ersoz et al, 2008;Zhu et al, 2008).…”

Section: Introductionmentioning

confidence: 99%