Development of a multiple-hybrid population for genome-wide association studies: theoretical consideration and genetic mapping of flowering traits in maize

Wang, Hui; Xu, Cheng; Liu, Xiaogang; Xu, Xiaojie; Wang, Shanhong; Xie, Chuanxiao; Li, Wenxue; Zou, Cheng; Xu, Yunbi

doi:10.1038/srep40239

Cited by 29 publications

(30 citation statements)

References 95 publications

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“…PH4CV was the paternal parent of XY335, a widely cultivated hybrid generated by the Pioneer Technology Co., Tieling, Jilin Province, China ( Gu et al, 2017 ). The P9-10 was derived from the hybrid PN78599 (also called P78599) by using bicyclic breeding strategy ( Wang et al, 2017 ). Another elite inbred line Y1518, a perfect material for maize transformation, was also applied in this study ( Zhou et al, 1999 ).…”

Section: Methodsmentioning

confidence: 99%

QTL Mapping in Three Connected Populations Reveals a Set of Consensus Genomic Regions for Low Temperature Germination Ability in Zea mays L.

Wang

et al. 2018

Front. Plant Sci.

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Improving seed vigor in response to cold stress is an important breeding objective in maize that allows early sowing. Using two cold tolerant inbred lines 220 and P9-10 and two susceptible lines Y1518 and PH4CV, three connected F2:3 populations were generated for detecting quantitative trait locus (QTL) related to seed low-temperature germination ability. At 10°C, two germination traits (emergence rate and germination index) were collected from a sand bed and three seedling traits (seedling root length, shoot length, and total length) were extracted from paper rolls. Significant correlations were found among all traits in all populations. Via single-population analysis, 43 QTL were detected with explained phenotypic variance of 0.62%∼39.44%. Seventeen QTL explained more than 10% phenotypic variance; of them sixteen (94.12%) inherited favorable alleles from the tolerant lines. After constructing a consensus map, three meta-QTL (mQTL) were identified to include at least two initial QTL from different populations. mQTL1-1 included seven initial QTL for both germination and seedling traits; with three explaining more than 30% phenotypic variance. mQTL2-1 and mQTL9-1 covered two to three initial QTL. The favorable alleles of the QTL within these three mQTL regions were all inherited from the tolerant line 220 and P9-10. These results provided a basis for cloning of genes underlying the mQTL regions to uncover the molecular mechanisms of maize cold tolerance during germination.

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Section: Methodsmentioning

confidence: 99%

QTL Mapping in Three Connected Populations Reveals a Set of Consensus Genomic Regions for Low Temperature Germination Ability in Zea mays L.

Wang

et al. 2018

Front. Plant Sci.

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“…GWA provides an efficient method to search for ADG-related genes in pigs. GWA studies are commonly based on single marker analysis and fixed-SNP-effect MLM [ 14 ]. These methods, however, are limited by the over-strict Bonferroni correction of multiple tests.…”

Section: Discussionmentioning

confidence: 99%

“…Common GWA methods are based on single marker analysis and fixed-SNP-effect MLM [ 14 ]. These methods are limited by the over-strict correction (Bonferroni correction) of multiple tests.…”

Section: Methodsmentioning

confidence: 99%

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Genome-wide association study reveals genetic loci and candidate genes for average daily gain in Duroc pigs

Quan

Ding

Wang

et al. 2018

Asian-Australas J Anim Sci

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ObjectiveAverage daily gain (ADG) is an important target trait of pig breeding programs. We aimed to identify single nucleotide polymorphisms (SNPs) and genomic regions that are associated with ADG in the Duroc pig population.MethodsWe performed a genome-wide association study involving 390 Duroc boars and by using the PorcineSNP60K Beadchip and two linear models.ResultsAfter quality control, we detected 3,5971 SNPs, which included seven SNPs that are significantly associated with the ADG of pigs. We identified six quantitative trait loci (QTL) regions for ADG. These QTLs included four previously reported QTLs on Sus scrofa chromosome (SSC) 1, SSC5, SSC9, and SSC13, as well as two novel QTLs on SSC6 and SSC16. In addition, we selected six candidate genes (general transcription factor 3C polypeptide 5, high mobility group AT-hook 2, nicotinamide phosphoribosyltransferase, oligodendrocyte transcription factor 1, pleckstrin homology and RhoGEF domain containing G4B, and ENSSSCG00000031548) associated with ADG on the basis of their physiological roles and positional information. These candidate genes are involved in skeletal muscle cell differentiation, diet-induced obesity, and nervous system development.ConclusionThis study contributes to the identification of the casual mutation that underlies QTLs associated with ADG and to future pig breeding programs based on marker-assisted selection. Further studies are needed to elucidate the role of the identified candidate genes in the physiological processes involved in ADG regulation.

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“…Korte & Farlow (2013) suggest that a way to mitigate the small sample effect is to account for large phenotypic variability. Thus, as we used hybrids rather than inbred lines, a series of different allelic combinations can occur, increasing the genetic variants with heterozygous loci and thereby allowing to find better results in GWAS analysis (Wang et al, 2017). This reflected in the number of significant SNPs identified by heterozygous (dis)advantage model, which was about three times higher than the additive model.…”

Section: Candidate Genes Related To the Maize Responsiveness To A Brmentioning

confidence: 99%

Maize responsiveness to <i>Azospirillum brasilense</i>: insights into genetic control and genomic prediction

Vidotti¹

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Maize responsiveness to Azospirillum brasilense: insights into genetic control and genomic prediction The inoculation with Azospirillum brasilense is one of the main strategies to supplement the inorganic inputs of nitrogen (N) and to increase the root development in maize. However, the beneficial inoculation effects are not always reached, which, in part, is due to genotypic variation in the plant host, resulting in different degrees of outcome. In this context, we aimed to study the genetic control and genomic prediction of maize traits related to the responsiveness to A. brasilense inoculation. For this, 118 maize hybrids were conducted under N stress and N stress plus A. brasilense treatments in controlled conditions over 2016 and 2017 seasons. We evaluated root and shoot traits and performed diallel analyses, association mapping, and genomic prediction methods considering 59,215 Single-Nucleotide Polymorphism (SNP) markers. Our results revealed a quantitative inheritance of the partnership-related maize traits, with both additive and non-additive genetic effects involved in the genetic control. Furthermore, several candidate genes were identified for the maize-A. brasilense association, especially with heterozygous (dis)advantage effects. In general, the prediction accuracies were higher mostly for the inoculated treatment compared to the non-inoculated. Finally, our findings enable a deeper understanding towards the genetic basis of the maize responsiveness to A. brasilense and may support plant breeders to establish selection strategies aiming the development of superior genotypes for this association.

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Development of a multiple-hybrid population for genome-wide association studies: theoretical consideration and genetic mapping of flowering traits in maize

Cited by 29 publications

References 95 publications

QTL Mapping in Three Connected Populations Reveals a Set of Consensus Genomic Regions for Low Temperature Germination Ability in Zea mays L.

QTL Mapping in Three Connected Populations Reveals a Set of Consensus Genomic Regions for Low Temperature Germination Ability in Zea mays L.

Genome-wide association study reveals genetic loci and candidate genes for average daily gain in Duroc pigs

Maize responsiveness to <i>Azospirillum brasilense</i>: insights into genetic control and genomic prediction

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