Genetic Architecture of a Rice Nested Association Mapping Population

Fragoso, Christopher A; Moreno, Marlene Aparecida; Wang, Zuoheng; Heffelfinger, Christopher; Arbelaez, Lady Johanna; Aguirre, John A; Franco, Natalia; Romero, Luz Elena; Labadie, Karine; Zhao, Hongyu; Dellaporta, Stephen L.; Lorieux, Mathias

doi:10.1534/g3.117.041608

Cited by 63 publications

(49 citation statements)

References 86 publications

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“…Most of the studies reported the genetic maps between a range of 600–1500 loci in biparental populations, except a WGRS based genetic map with 8869 loci in 3120 cM (Agarwal et al , ). In other crops, similar studies using NAM populations successfully dissected the genetics of complex traits and facilitated candidate gene discovery, such as in soybean (Song et al , ; Xavier et al , ), maize (McMullen et al , ; Yu et al , ), wheat (Hu et al , ; Jordan et al , ) and rice (Fragoso et al , ). In most of these studies, the GWAS analysis was performed in NAM populations instead of constructing genetic maps.…”

Section: Discussionmentioning

confidence: 99%

Nested‐association mapping (NAM)‐based genetic dissection uncovers candidate genes for seed and pod weights in peanut (Arachis hypogaea)

Gangurde

Wang

Shasidhar

et al. 2019

Plant Biotechnology Journal

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email baozhu.guo@usda.gov (B. G.); Tel 91-40-30713345; fax 91-40-30713074; email r.k.varshney@cgiar.org (R. K. V.)) † These authors contributed equally to this study. SummaryMultiparental genetic mapping populations such as nested-association mapping (NAM) have great potential for investigating quantitative traits and associated genomic regions leading to rapid discovery of candidate genes and markers. To demonstrate the utility and power of this approach, two NAM populations, NAM_Tifrunner and NAM_Florida-07, were used for dissecting genetic control of 100-pod weight (PW) and 100-seed weight (SW) in peanut. Two high-density SNP-based genetic maps were constructed with 3341 loci and 2668 loci for NAM_Tifrunner and NAM_Florida-07, respectively. The quantitative trait locus (QTL) analysis identified 12 and 8 major effect QTLs for PW and SW, respectively, in NAM_Tifrunner, and 13 and 11 major effect QTLs for PW and SW, respectively, in NAM_Florida-07. Most of the QTLs associated with PW and SW were mapped on the chromosomes A05, A06, B05 and B06. A genomewide association study (GWAS) analysis identified 19 and 28 highly significant SNP-trait associations (STAs) in NAM_Tifrunner and 11 and 17 STAs in NAM_Florida-07 for PW and SW, respectively. These significant STAs were co-localized, suggesting that PW and SW are co-regulated by several candidate genes identified on chromosomes A05, A06, B05, and B06. This study demonstrates the utility of NAM population for genetic dissection of complex traits and performing highresolution trait mapping in peanut.

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Section: Discussionmentioning

confidence: 99%

Nested‐association mapping (NAM)‐based genetic dissection uncovers candidate genes for seed and pod weights in peanut (Arachis hypogaea)

Gangurde

Wang

Shasidhar

et al. 2019

Plant Biotechnology Journal

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“…In maize, where this technique was developed, it was first used to map genes associated with flowering time (Buckler et al ., ; Figure ). Since then it has been extended for use in rice (Fragoso et al ., ), wheat (Bajgain et al ., ) and barley (Maurer et al ., ).…”

Section: Finding Associations Between Genotype and Phenotype: Linkagementioning

confidence: 99%

Evolutionary and ecological functional genomics, from lab to the wild

2018

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Summary Plant phenotypes are the result of both genetic and environmental forces that act to modulate trait expression. Over the last few years, numerous approaches in functional genomics and systems biology have led to a greater understanding of plant phenotypic variation and plant responses to the environment. These approaches, and the questions that they can address, have been loosely termed evolutionary and ecological functional genomics (EEFG), and have been providing key insights on how plants adapt and evolve. In particular, by bringing these studies from the laboratory to the field, EEFG studies allow us to gain greater knowledge of how plants function in their natural contexts.

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“…These secondary mapping populations are required to facilitate more comprehensive analysis of target QTLs (Yano, 2001). More recently in rice, multi-parent populations called multi-parent advanced generation intercross (MAGIC; Bandillo et al, 2013), CSSLs (Bessho-Uehara et al, 2017;Ogawa et al, 2016) and nested-association mapping populations (Fragoso et al, 2017) have been used for QTL mapping.…”

Section: Approaches To Qtl Mappingmentioning

confidence: 99%

Association mapping in rice: basic concepts and perspectives for molecular breeding

Verdeprado

Kretzschmar

Begum

et al. 2018

Plant Production Science

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In the last decade, association mapping (AM) has become a well-established method to detect genes and quantitative trait loci (QTLs) associated with agronomically important traits. The identification of a large number of single nucleotide polymorphisms (SNPs) from genome sequencing and concurrent development of high-throughput genotyping platforms has led to AM being widely used for a range of crops. These technologies have been used in rice (Oryza sativa) to explore the abundant diversity and there is enormous potential to identify novel QTLs for traits of interest. Due to the availability of cost-effective high-throughput SNP genotyping methods and rapid developments in rice genomics, it is inevitable that these AM approaches will become more popular in the future, especially in the context of genome-wide association studies (GWASs). In this paper, we review the fundamental concepts, critical considerations and limitations of AM focusing on rice, and reiterate the importance of accurate phenotypic data. We also include a section about connecting GWAS to molecular breeding, covering practical consideration for breeders, which is required to use GWAS results in actual rice molecular breeding programs and which has not received adequate attention in the scientific literature.

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Genetic Architecture of a Rice Nested Association Mapping Population

Cited by 63 publications

References 86 publications

Nested‐association mapping (NAM)‐based genetic dissection uncovers candidate genes for seed and pod weights in peanut (Arachis hypogaea)

Nested‐association mapping (NAM)‐based genetic dissection uncovers candidate genes for seed and pod weights in peanut (Arachis hypogaea)

Evolutionary and ecological functional genomics, from lab to the wild

Association mapping in rice: basic concepts and perspectives for molecular breeding

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