Detection of epistatic and environmental interaction <scp>QTL</scp>s for leaf orientation‐related traits in maize

Shi, Yong; Wang, Xiaobo; Guo, Shulei; Ren, Zhenzhen; Ku, Lixia; Zhu, Yuguang; Li, Guohui; Jing, Qi; Ren, Zhaobin; Chen, Yanhui

doi:10.1111/pbr.12431

Cited by 10 publications

(5 citation statements)

References 45 publications

(112 reference statements)

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“…In maize, statistical epistasis is rarely observed in QTL analyses (Edwards et al ., ; Stuber et al ., ; Briggs et al ., ) or in genome‐wide scans in panels of inbred maize lines (Wallace et al ., ) – but see Shi et al . () for epistatic effects in leaf orientation – but is more commonly found when individual cloned QTLs are placed into otherwise isogenic maize or teosinte backgrounds (Doebley et al ., ; Weber et al ., ; Studer & Doebley, ). As variation both in the genotype and phenotype of a causative locus must occur in a mapping population, studies focusing on maize specifically may fail to observe differences.…”

Section: Genetic Interactions and Selection During Maize Domesticationmentioning

confidence: 99%

Maize domestication and gene interaction

Stitzer

Ross‐Ibarra

2018

New Phytologist

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Contents Summary 395 I. Introduction 395 II. The genetic basis of maize domestication 396 III. The tempo of maize domestication 401 IV. Genetic interactions and selection during maize domestication 401 V. Gene networks of maize domestication alleles 404 VI. Implications of gene interactions on evolution and selection404 VII. Conclusions 405 Acknowledgements 405 References 405 SUMMARY: Domestication is a tractable system for following evolutionary change. Under domestication, wild populations respond to shifting selective pressures, resulting in adaptation to the new ecological niche of cultivation. Owing to the important role of domesticated crops in human nutrition and agriculture, the ancestry and selection pressures transforming a wild plant into a domesticate have been extensively studied. In Zea mays, morphological, genetic and genomic studies have elucidated how a wild plant, the teosinte Z. mays subsp. parviglumis, was transformed into the domesticate Z. mays subsp. mays. Five major morphological differences distinguish these two subspecies, and careful genetic dissection has pinpointed the molecular changes responsible for several of these traits. But maize domestication was a consequence of more than just five genes, and regions throughout the genome contribute. The impacts of these additional regions are contingent on genetic background, both the interactions between alleles of a single gene and among alleles of the multiple genes that modulate phenotypes. Key genetic interactions include dominance relationships, epistatic interactions and pleiotropic constraint, including how these variants are connected in gene networks. Here, we review the role of gene interactions in generating the dramatic phenotypic evolution seen in the transition from teosinte to maize.

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Section: Genetic Interactions and Selection During Maize Domesticationmentioning

confidence: 99%

Maize domestication and gene interaction

Stitzer

Ross‐Ibarra

2018

New Phytologist

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“…Based on a published review (Cao et al, 2022), the QTL information have been reported for LA-related traits (Lu et al, Frontiers in Genetics frontiersin.org 03 Duan et al 10.3389/fgene.2022.1004211 2007; Ku et al, 2010;Tian et al, 2011;Ku et al, 2012;Chen et al, 2015;Ding et al, 2015;Li et al, 2015;Ku et al, 2016;Pan et al, 2017;Shi et al, 2017;Wang et al, 2017;Dzievit et al, 2019;Liu et al, 2019;Zhang et al, 2019;Tang et al, 2021). The QTL information (Chromosome, LOD, R 2 , Confidence Interval and so on) were summarized from eighteen studies published in the lasted 15 years.…”

Section: Meta-analysesmentioning

confidence: 99%

“…Oryza sativa TGA2 (OsTGA2) can directly regulate defenserelated genes (Moon et al, 2018). The key points in the regulation of sunflower resistance by TGA may be involved in the resistance of sunflower to Verticillium dahliae (Guo et al, 2017). In addition, ROXY can be used as TGA-dependent promoter to control the negative regulators of detoxification genes in A. thaliana (Huang et al, 2016).…”

Section: Introductionmentioning

confidence: 99%

Accelerating Genetic Gain for Key Traits Using Genome-Wide Association Studies and Genomic Selection: Promising Breeding Tools for Sustainable Agriculture

Kumar,

Juliana,

Chandra Mishra

2024

Frontiers Research Topics

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Frontiers is more than just an open access publisher of scholarly articles: it is a pioneering approach to the world of academia, radically improving the way scholarly research is managed. The grand vision of Frontiers is a world where all people have an equal opportunity to seek, share and generate knowledge. Frontiers provides immediate and permanent online open access to all its publications, but this alone is not enough to realize our grand goals. Frontiers journal seriesThe Frontiers journal series is a multi-tier and interdisciplinary set of openaccess, online journals, promising a paradigm shift from the current review, selection and dissemination processes in academic publishing. All Frontiers journals are driven by researchers for researchers; therefore, they constitute a service to the scholarly community. At the same time, the Frontiers journal series operates on a revolutionary invention, the tiered publishing system, initially addressing specific communities of scholars, and gradually climbing up to broader public understanding, thus serving the interests of the lay society, too. Dedication to qualityEach Frontiers article is a landmark of the highest quality, thanks to genuinely collaborative interactions between authors and review editors, who include some of the world's best academicians. Research must be certified by peers before entering a stream of knowledge that may eventually reach the public -and shape society; therefore, Frontiers only applies the most rigorous and unbiased reviews. Frontiers revolutionizes research publishing by freely delivering the most outstanding research, evaluated with no bias from both the academic and social point of view. By applying the most advanced information technologies, Frontiers is catapulting scholarly publishing into a new generation. What are Frontiers Research Topics?Frontiers Research Topics are very popular trademarks of the Frontiers journals series: they are collections of at least ten articles, all centered on a particular subject. With their unique mix of varied contributions from Original Research to Review Articles, Frontiers Research Topics unify the most influential researchers, the latest key findings and historical advances in a hot research area.

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“…Based on a published review (Cao et al, 2022), the QTL information have been reported for LA-related traits (Lu et al, 2007;Ku et al, 2010;Tian et al, 2011;Ku et al, 2012;Chen et al, 2015;Ding et al, 2015;Hu et al, 2015;Li et al, 2015;Yang et al, 2015;Ku et al, 2016;Pan et al, 2017;Shi et al, 2017;Wang et al, 2017;Dzievit et al, 2019;Liu et al, 2019;Zhang et al, 2019;Zhang et al, 2020;Tang et al, 2021). The QTL information (Chromosome, LOD, R 2 , Confidence Interval and so on) were summarized from eighteen studies published in the lasted 15 years.…”

Section: Meta-analysesmentioning

confidence: 99%

Candidate loci for leaf angle in maize revealed by a combination of genome-wide association study and meta-analysis

Duan

Li²,

Sun³

et al. 2022

Front. Genet.

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Leaf angle (LA) is a key component of maize plant architecture that can simultaneously govern planting density and improve final yield. However, the genetic mechanisms underlying LA have not been fully addressed. To broaden our understanding of its genetic basis, we scored three LA-related traits on upper, middle, and low leaves of 492 maize inbred lines in five environments. Phenotypic data revealed that the three LA-related traits were normally distributed, and significant variation was observed among environments and genotypes. A genome-wide association study (GWAS) was then performed to dissect the genetic factors that control natural variation in maize LA. In total, 85 significant SNPs (involving 32 non-redundant QTLs) were detected (p ≤ 2.04 × 10–6), and individual QTL explained 4.80%–24.09% of the phenotypic variation. Five co-located QTL were detected in at least two environments, and two QTLs were co-located with multiple LA-related traits. Forty-seven meta-QTLs were identified based on meta-analysis combing 294 LA-related QTLs extracted from 18 previously published studies, 816 genes were identified within these meta-QTLs, and seven co-located QTLs were jointly identified by both GWAS and meta-analysis. ZmULA1 was located in one of the co-located QTLs, qLA7, and its haplotypes, hap1 and hap2, differed significantly in LA-related traits. Interestingly, the temperate materials with hap2 had smallest LA. Finally, we also performed haplotype analysis using the reported genes that regulate LA, and identified a lot of maize germplasms that aggregated favorable haplotypes. These results will be helpful for elucidating the genetic basis of LA and breeding new maize varieties with ideal plant architecture.

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Detection of epistatic and environmental interaction QTLs for leaf orientation‐related traits in maize

Cited by 10 publications

References 45 publications

Maize domestication and gene interaction

Maize domestication and gene interaction

Accelerating Genetic Gain for Key Traits Using Genome-Wide Association Studies and Genomic Selection: Promising Breeding Tools for Sustainable Agriculture

Candidate loci for leaf angle in maize revealed by a combination of genome-wide association study and meta-analysis

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