Genome-Wide Association Study Reveals Novel Genomic Regions Associated With High Grain Protein Content in Wheat Lines Derived From Wild Emmer Wheat

Liu, Jia; Huang, Lin; Wang, Changquan; Liu, Yaxi; Yan, Zehong; Wang, Zhenzhen; Xiang, Lan; Zhong, Xu; Gong, Fangyi; Zheng, Youliang; Liu, Dengcai; Wu, Bihua

doi:10.3389/fpls.2019.00464

Cited by 32 publications

(40 citation statements)

References 71 publications

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“…The sequences of the significant DArT‐seq markers identified by GWAS were used to perform BLASTn searches against the International Wheat Genome Sequencing Consortium (IWGSC) RefSeq v1.0 with annotation of genes available in the URGI wheat database (https://wheat-urgi.versailles.inra.fr/Seq-Repository/Annotations, accessed 15 Oct. 2019) to determine the physical position of each marker, and identify genes within a region 2500 bp upstream and 2500 bp downstream of this position (Liu et al, 2017; Wu et al, 2017; Juliana et al, 2018; Liu et al 2019). Candidate genes were annotated using Oryza sativa and Arabidopsis thaliana as background species at P < 10 −5 using KOBAS 3.0 (Wu et al, 2006).…”

Section: Methodsmentioning

confidence: 99%

Dissection of Phenotypic and Genetic Variation of Drought‐Related Traits in Diverse Chinese Wheat Landraces

Lin

Tang

et al. 2019

The Plant Genome

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The Plant Genome W heat (Triticum aestivum L.) which originated in the Fertile Crescent has been domesticated for some 10,000 yr (Lev-Yadun et al., 2000). Currently, wheat is one of the most widely planted crops, supplying approximately 30% of the human population. Although wheat is mainly grown on rainfed land, approximately 37% of the cropping area in developing countries consists of semiarid environments, where drought imposes a primary constraint on wheat production (Qayyum et al., 2011; Sadok, 2017; Sinclair, 2011). As the climate continues to change, drought is predicted to become more severe and more widely distributed, and thus will probably further limit crop growth and reduce yields (

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Section: Methodsmentioning

confidence: 99%

Dissection of Phenotypic and Genetic Variation of Drought‐Related Traits in Diverse Chinese Wheat Landraces

Lin

Tang

et al. 2019

The Plant Genome

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“…The OFP gene expression data were obtained from transcriptome data for Chinese Spring wheat seedlings under drought and heat stress conditions [ 33 ]. Chinese Spring wheat transcriptome data under GA, jasmonic acid, abscisic acid, salicylic acid, and cytokinin treatment were used to obtain OFP gene expression data from the Introduction to the Triticeae Multi-omics Center database [ 34 ]. The expression data were used to construct a heat map using TBtool [ 35 ].…”

Section: Methodsmentioning

confidence: 99%

Genome-Wide Characterization of OFP Family Genes in Wheat (Triticum aestivum L.) Reveals That TaOPF29a-A Promotes Drought Tolerance

Wang

Cao

Wang

et al. 2020

BioMed Research International

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OVATE family proteins (OFPs) are plant-specific transcription factors that play important roles in plant development. Although common wheat (Triticum aestivum L.) is a major staple food worldwide, OFPs have not been systematically analyzed in this important crop. Here, we performed a genome-wide survey of OFP genes in wheat and identified 100 genes belonging to 34 homoeologous groups. Arabidopsis thaliana, rice (Oryza sativa), and wheat OFP genes were divided into four subgroups based on their phylogenetic relationships. Structural analysis indicated that only four TaOFPs contain introns. We mapped the TaOFP genes onto the wheat chromosomes and determined that TaOFP17 was duplicated in this crop. A survey of cis-acting elements along the promoter regions of TaOFP genes suggested that subfunctionalization of homoeologous genes might have occurred during evolution. The TaOFPs were highly expressed in wheat, with tissue- or organ-specific expression patterns. In addition, these genes were induced by various hormone and stress treatments. For instance, TaOPF29a-A was highly expressed in roots in response to drought stress. Wheat plants overexpressing TaOPF29a-A had longer roots and higher dry weights than nontransgenic plants under drought conditions, suggesting that this gene improves drought tolerance. Our findings provide a starting point for further functional analysis of this important transcription factor family and highlight the potential of using TaOPF29a-A to genetically engineer drought-tolerant crops.

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“…The same set of 161 advanced lines (Liu et al, 2019) derived from a cross between CN16 and D1 were used in the present study. Wheat plants were arranged in the field using a randomized complete block design with three replicates over two growing seasons (2015 and 2016) at the Chongzhou (2015CZ and 2016CZ) and Wenjiang (2015WJ and 2016WJ) experimental stations of Sichuan Agricultural University, China (Liu et al, 2019). Individual plants were spaced 10 cm apart within a 2 m row with 30 cm between rows.…”

Section: Plant Materials and Experimental Designmentioning

confidence: 99%

“…Genome-wide association analysis (GWAS) has been widely used for deciphering the genetic basis of multiple traits in crops (Su et al, 2016;Wang et al, 2016;Ates et al, 2018;Liu et al, 2019). It was available to study QTLs related to agronomically important traits in large sets of germplasm resources such as landraces (Liu et al, 2017), elite cultivars (Sukumaran et al, 2015), and advanced breeding lines (Wang et al, 2017) as well as backbone parents and their derived lines (Yu and Tian, 2012;Yu et al, 2014;Xiao et al, 2016;Liu et al, 2019). In wheat, GWAS has been extensively applied to reveal genomic regions controlling traits such as GPC (Liu et al, 2019), grain ionome (Fatiukha et al, 2020), and yield-related traits (Tadesse et al, 2015).…”

Section: Introductionmentioning

confidence: 99%

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Genome-Wide Association Study for Grain Micronutrient Concentrations in Wheat Advanced Lines Derived From Wild Emmer

Liu

Huang

et al. 2021

Front. Plant Sci.

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Wheat is one of the important staple crops as the resources of both food and micronutrient for most people of the world. However, the levels of micronutrients (especially Fe and Zn) in common wheat are inherently low. Biofortification is an effective way to increase the micronutrient concentration of wheat. Wild emmer wheat (Triticum turgidum ssp. dicoccoides, AABB, 2n = 4x = 28) is an important germplasm resource for wheat micronutrients improvement. In the present study, a genome-wide association study (GWAS) was performed to characterize grain iron, zinc, and manganese concentration (GFeC, GZnC, and GMnC) in 161 advanced lines derived from wild emmer. Using both the general linear model and mixed linear model, we identified 14 high-confidence significant marker-trait associations (MTAs) that were associated with GFeC, GZnC, and GMnC of which nine MTAs were novel. Six MTAs distributed on chromosomes 3B, 4A, 4B, 5A, and 7B were significantly associated with GFeC. Three MTAs on 1A and 2A were significantly associated with GZnC and five MTAs on 1B were significantly associated with GMnC. These MTAs show no negative effects on thousand kernel weight (TKW), implying the potential value for simultaneous improvement of micronutrient concentrations and TKW in breeding. Meanwhile, the GFeC, GZnC and GMnC are positively correlated, suggesting that these traits could be simultaneously improved. Genotypes containing high-confidence MTAs and 61 top genotypes with a higher concentration of grain micronutrients were recommended for wheat biofortification breeding. A total of 38 candidate genes related to micronutrient concentrations were identified. These candidates can be classified into four main groups: enzymes, transporter proteins, MYB transcription factor, and plant defense responses proteins. The MTAs and associated candidate genes provide essential information for wheat biofortification breeding through marker-assisted selection (MAS).

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Genome-Wide Association Study Reveals Novel Genomic Regions Associated With High Grain Protein Content in Wheat Lines Derived From Wild Emmer Wheat

Cited by 32 publications

References 71 publications

Dissection of Phenotypic and Genetic Variation of Drought‐Related Traits in Diverse Chinese Wheat Landraces

Dissection of Phenotypic and Genetic Variation of Drought‐Related Traits in Diverse Chinese Wheat Landraces

Genome-Wide Characterization of OFP Family Genes in Wheat (Triticum aestivum L.) Reveals That TaOPF29a-A Promotes Drought Tolerance

Genome-Wide Association Study for Grain Micronutrient Concentrations in Wheat Advanced Lines Derived From Wild Emmer

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