Genome-wide association study of pre-harvest sprouting resistance in Chinese wheat founder parents

Lin, Yu; Liu, Shihang; Liu, Yaxi; Liu, Yujiao; Chen, Guoyue; Xu, Jie; Deng, Mei; Jiang, Qiantao; Wei, Yuming; Lu, Yanli; Zheng, Yu

doi:10.1590/1678-4685-gmb-2016-0207

Cited by 15 publications

(9 citation statements)

References 82 publications

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“…In our study the mixed effects models fitted better for most of our traits, while only a few traits were found to have better associations with GLM models where the K matrix was not taken into account. These findings are in accordance with those of Wang et al [36], Nigro et al [37], or Lin et al [35], who reported that MLM models were more appropriate for association studies in maize and wheat.…”

Section: Discussionsupporting

confidence: 93%

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Association Mapping Between Candidate Gene SNP and Production and Oil Quality Traits in Interspecific Oil Palm Hybrids

Astorkia

Hernández

Bocs

et al. 2019

Plants

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Oil palm production is gaining importance in Central and South America. However, the main species Elaeis guineensis (Eg) is suffering severely from bud rod disease, restricting the potential cultivation areas. Therefore, breeding companies have started to work with interspecific Elaeis oleifera × Eg (Eo × Eg) hybrids which are tolerant to this disease. We performed association studies between candidate gene (CG) single nucleotide polymorphisms (SNP) and six production and 19 oil quality traits in 198 accessions of interspecific oil palm hybrids from five different origins. For this purpose, barcoded amplicons of initially 167 CG were produced from each genotype and sequenced with Ion Torrent. After sequence cleaning 115 SNP remained targeting 62 CG. The influence of the origins on the different traits was analyzed and a genetic diversity study was performed. Two generalized linear models (GLM) with principle component analysis (PCA) or structure (Q) matrixes as covariates and two mixed linear models (MLM) which included in addition a Kinship (K) matrix were applied for association mapping using GAPIT. False discovery rate (FDR) multiple testing corrections were applied in order to avoid Type I errors. However, with FDR adjusted p values no significant associations between SNP and traits were detected. If using unadjusted p values below 0.05, seven of the studied CG showed potential associations with production traits, while 23 CG may influence different quality traits. Under these conditions the current approach and the detected candidate genes could be exploited for selecting genotypes with superior CG alleles in Marker Assisted Selection systems.

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Section: Discussionsupporting

confidence: 93%

“…After the analysis, the coincidence of observed and expected p values was visualized in a QQ plot for each trait. Several authors have used these QQ plots to determine the best fitting models visually [33,34,35].…”

Section: Discussionmentioning

confidence: 99%

Association Mapping Between Candidate Gene SNP and Production and Oil Quality Traits in Interspecific Oil Palm Hybrids

Astorkia

Hernández

Bocs

et al. 2019

Plants

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“…However, the markers associated with each individual environment did not overlap with the BLUE_ALL associated markers. The results may reflect the small size of the study panel [ 65 – 69 ]. Considering the LD decay distance (6.4 cM) in the present study and marker position in the integrated map, a total of 16 QTL were detected (Table 3 , Additional file 6 ).…”

Section: Discussionmentioning

confidence: 99%

“…The power of QTL detection by GWAS depends on sample size, number of markers, high LD and trait heritability [ 20 , 62 , 68 ]. The number of landraces (93) used in the current study was larger than that used for genome-wide association mapping of resistance to pre-harvest sprouting (80 Chinese wheat founder parents) [ 65 ], rust resistance mechanisms (33 orchardgrass accessions) [ 67 ], phenotypic traits (81 Canadian western spring wheat cultivars) [ 68 ], late maturity α-amylase activity (91 synthetic hexaploid wheat accessions) [ 69 ], and comparable to the 93 bread wheat accessions used for mapping agronomic traits [ 66 ]. However, the population size of the present study was smaller than that of several previous studies, which would lower the power of QTL detection.…”

Section: Discussionmentioning

confidence: 99%

Characterization of molecular diversity and genome-wide association study of stripe rust resistance at the adult plant stage in Northern Chinese wheat landraces

Yao

Xue-mei

et al. 2019

BMC Genet

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Background: Stripe rust is a serious fungal disease of wheat (Triticum aestivum L.) caused by Puccinia striiformis f. sp. tritici (Pst), which results in yield reduction and decreased grain quality. Breeding for genetic resistance to stripe rust is the most cost-effective method to control the disease. In the present study, a genome-wide association study (GWAS) was conducted to identify markers linked to stripe rust resistance genes (or loci) in 93 Northern Chinese wheat landraces, using Diversity Arrays Technology (DArT) and simple sequence repeat (SSR) molecular marker technology based on phenotypic data from two field locations over two growing seasons in China. Results: Seventeen accessions were verified to display stable and high levels of adult plant resistance (APR) to stripe rust via multi-environment field assessments. Significant correlations among environments and high heritability were observed for stripe rust infection type (IT) and disease severity (DS). Using mixed linear models (MLM) for the GWAS, a total of 32 significantly associated loci (P < 0.001) were detected. In combination with the linkage disequilibrium (LD) decay distance (6.4 cM), 25 quantitative trait loci (QTL) were identified. Based on the integrated map of previously reported genes and QTL, six QTL located on chromosomes 4A, 6A and 7D were mapped far from resistance regions identified previously, and represent potentially novel stripe rust resistance loci at the adult plant stage. Conclusions: The present findings demonstrated that identification of genes or loci linked to significant markers in wheat by GWAS is feasible. Seventeen elite accessions conferred with stable and high resistance to stripe rust, and six putative newly detected APR loci were identified among the 93 Northern Chinese wheat landraces. The results illustrate the potential for acceleration of molecular breeding of wheat, and also provide novel sources of stripe rust resistance with potential utility in the breeding of improved wheat cultivars.

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“…Marker-assisted selection (MAS) is considered to be an excellent approach for the precision breeding of crops, as it improves breeding efficiency and predictability, and thus accelerates the progress of breeding programs (Collard and Mackill, 2008). Furthermore, genome-wide association study (GWAS) has been an effective and powerful tool in the search for genes underlying complex traits in plants, including Arabidopsis (Verslues et al, 2014;Bac-Molenaar et al, 2016), Aegilops tauschii (Arora et al, 2017;Liu et al, 2015a;Liu et al, 2015b), maize (Zea mays L.; Yang et al, 2014), and wheat (Lin et al, 2017;Liu et al, 2017;Oyiga et al, 2017;Valluru et al, 2017). In plants, traits characterized by GWASs include those associated with general plant morphology, yield, and biotic and abiotic resistance or tolerance (Verslues et al, 2014;Bac-Molenaar et al, 2016;Liu et al, 2017;Oyiga et al, 2017;Valluru et al, 2017;Zhou et al, 2017).…”

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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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Genome-wide association study of pre-harvest sprouting resistance in Chinese wheat founder parents

Cited by 15 publications

References 82 publications

Association Mapping Between Candidate Gene SNP and Production and Oil Quality Traits in Interspecific Oil Palm Hybrids

Association Mapping Between Candidate Gene SNP and Production and Oil Quality Traits in Interspecific Oil Palm Hybrids

Characterization of molecular diversity and genome-wide association study of stripe rust resistance at the adult plant stage in Northern Chinese wheat landraces

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

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