Association of candidate genes with heading date in a diverse Dactylis glomerata population

Zhao, Xinxin; Bushman, B. Shaun; Zhang, Xinquan; Robbins, Matthew D.; Larson, Steven R.; Robins, Joseph G.; Thomas, Aaron J.

doi:10.1016/j.plantsci.2017.10.002

Cited by 14 publications

(26 citation statements)

References 44 publications

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“…The GWASpoly in R is software tailored for polyploids, which that can model different types of polyploid gene actions in GWAS, including additive, simplex dominant, and duplex dominant actions (Rosyara, De Jong, Douches, & Endelman, 2016). This software has been tested in a simulated tetraploid population and successfully applied in potato (Solanum tuberosum L.), sunflower (Helianthus annuus L.), orchardgrass (Dactylis glomerata L.), wheat (Triticum aestivum L.), and white clover (Trifolium repens L.) for GWAS (Berdugo-Cely, Valbuena, Sánchez-Betancourt, Barrero, & Yockteng, 2017;Bock, Kantar, Caseys, Matthey-Doret, & Rieseberg, 2018;Inostroza et al, 2018;Phan et al, 2018;Rosyara et al, 2016;Zhao et al, 2017). However, this software has not been used for GWAS in sugarcane.…”

Section: Introductionmentioning

confidence: 99%

Genome‐wide association study of multiple yield traits in a diversity panel of polyploid sugarcane (Saccharum spp.)

et al. 2020

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Sugarcane (Saccharum spp.) is an important economic crop, contributing up to 80% of sugar and approximately 60% of biofuel globally. To meet the increased demand for sugar and biofuel supplies, it is critical to breed sugarcane cultivars with robust performance in yield traits. Therefore, dissection of causal DNA sequence variants is of great importance, as it provides genetic resources and fundamental information for crop improvement. In this study, we analyzed nine yield traits in a sugarcane diversity panel consisting of 308 accessions primarily selected from the World Collection of Sugarcane and Related Grasses. By genotyping the diversity panel via target enrichment sequencing, we identified a large number of sequence variants. Genome-wide association studies between the markers and traits were conducted, taking dosages and gene actions into consideration. In total, 217 nonredundant markers and 225 candidate genes were identified to be significantly associated with the yield traits, which can serve as a comprehensive genetic resource database for future gene identification, characterization, and selection for sugarcane improvement. We further investigated runs of homozygosity (ROH) in the sugarcane diversity panel. We characterized 282 ROHs and found that the occurrence of ROHs in the genome were nonrandom and probably under selection. The ROHs were associated with total weight and dry weight, and high ROHs resulted in a decrease in the two traits. This study suggests that genomic inbreeding has led to negative impacts on sugarcane yield. Abbreviations: DAPC, discriminant analysis of principal components; GWAS, genome-wide association study; indels, insertions and deletions; NGS, next-generation sequencing; NROH, total number of ROHs; ROH, run of homozygosity; SROH, sum total length of ROHs; SNP, single nucleotide polymorphisms; TES, target enrichment sequencing; WCSRG, world collection of sugarcane and related grasses. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

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Section: Introductionmentioning

confidence: 99%

Genome‐wide association study of multiple yield traits in a diversity panel of polyploid sugarcane (Saccharum spp.)

et al. 2020

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“…GWASpoly in R is a software tailored for polyploids, which could model different types of polyploid gene actions in GWAS, including additive, simplex dominant, and duplex dominant (Rosyara et al 2016). This software has been tested in a simulated tetraploid population, and successfully applied in potato, sunflower, orchardgrass and wheat for GWAS (Berdugo-Cely et al 2017; Bock et al 2018; Phan et al 2018; Rosyara et al 2016; Zhao et al 2017). However, this software has not been utilized for GWAS in sugarcane.…”

Section: Introductionmentioning

confidence: 99%

Genome-wide association study of multiple yield components in a diversity panel of polyploid sugarcane (Saccharum spp.)

Yang

Luo

Todd

et al. 2018

Preprint

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25Sugarcane (Saccharum spp.) is an important economic crop, contributes up to 80% of 26 sugar and approximately 60% bio-fuel globally. To meet the increased demand for sugar and 27 bio-fuel supplies, it is critical to breed sugarcane cultivars with robust performance in yield 28 components. Therefore, dissection of causal DNA sequence variants is of great importance by 29 providing genetic resources and fundamental information for crop improvement. In this study, 30 we evaluated and analyzed nine yield components in a sugarcane diversity panel consisting of 31 308 accessions primarily selected from the "world collection of sugarcane and related grasses". 32 By genotyping the diversity panel using target enrichment sequencing, we identified a large 33 number of sequence variants. Genome-wide association study between the markers and traits 34 were conducted with dosages and gene actions taken into consideration. In total, 217 non-35 redundant markers and 225 candidate genes were identified to be significantly associated with 36 the yield components, which can serve as a comprehensive genetic resource database for future 37 gene identification, characterization, and selection for sugarcane improvement. We further 38 investigated runs of homozygosity (ROH) in the sugarcane diversity panel. We characterized 282 39 ROHs, and found that the occurrence of ROH in the genome were non-random and probably 40 under selection. ROHs were associated with total weight and dry weight, and high ROHs 41 resulted in decrease of the two traits. This study approved that genomic inbreeding has led to 42 negative impacts on sugarcane yield. 43 GWAS 45 46As an important cash crop, sugarcane (Saccharum spp.) contributes up to 80% of sugar 48 and approximately 60% bio-fuel globally (Dahlquist 2013). To meet the increasing global 49 demand for sugar and bio-fuel, sugarcane harvest area in the world has increased from 22.7 to 50 26.8 million hectares in the last ten years (FAO 2016). However, cropping areas for sugarcane 51 could not be increased indefinitely due to the limited farming land areas and competition with 52 food crops. In order to sustainably improve sugarcane production, breeding sugarcane cultivars 53 with high performance for yield components is critical. Thus, evaluating yield components in 54 sugarcane germplasm and dissecting the genetic basis of causal sequence variants are of great 55 importance to fulfill this strategy by providing tools and genetic resources. 56 The Saccharum genus consists of two wild species (S. spontaneum and S. robustum) 57 and four cultivated species (S. officinarum, S. barberi, S. sinence, and S. edule) (Daniels and 58 Roach 1987). All the Saccharum species are readily intercrossed except sterile S. edule. Modern 59 sugarcane hybrids were primarily derived from inter-species hybridization between S. 60 spontaneum (2n = 40-128, x = 8) and S. officinarum (2n = 80, x = 10) followed by several 61 backcrosses with S. officinarum. Therefore, modern sugarcane hybrids have a chromoso...

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“…In recent years, association analysis in forage grasses is applied extensively for dissecting the genetic bases of different quantitative traits in several species such as perennial ryegrass ( Lolium perenne ) (Auzanneau et al ., 2011; Yu et al ., 2011; Tang et al ., 2013; Yu et al ., 2013), tall fescue ( Festuca arundinacea ) (Lou et al ., 2015; Sun et al ., 2015), and orchardgrass ( Dactylis glomerata L.) (Yan et al ., 2016; Zhao et al ., 2017; Abtahi et al ., 2018b). These studies have demonstrated that GWAS is an efficient technique for identifying genomic regions linked to the quantitative traits.…”

Section: Introductionmentioning

confidence: 99%

Genome-wide association study revealed loci linked to post-drought recovery and traits related to persistence of smooth bromegrass (Bromus inermis)

Saeidnia

Majidi

Mirlohi

2021

Preprint

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Association analysis has been proved as a powerful tool for genetic dissection of complex traits. This study was conducted to identify marker – trait associations for recovery, persistence, and as well as finding stable associations. In this study, a diverse panel of polycross derived progenies of smooth bromegrass was phenotyped under normal and water stress, during three consecutive years. Association analysis was performed between nine important agronomic traits along with three seasonal growth activity indices based on 535 SRAP markers. Population structure analysis identified five main subpopulations possessing significant genetic differences. Association analysis using mixed linear mode1 identified 339 and 233 marker-trait associations under normal and water stress environments, respectively. Some of these markers were associated with more than one trait; which can be attributed to pleiotropic effects or to a number of tightly linked genes affecting several traits. If the effectiveness of these markers in genetic control of these traits is validated, they could be potentially used for initiation of marker-assisted selection and targeted trait introgression of smooth bromegrass under normal and water stress environments.

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Association of candidate genes with heading date in a diverse Dactylis glomerata population

Cited by 14 publications

References 44 publications

Genome‐wide association study of multiple yield traits in a diversity panel of polyploid sugarcane (Saccharum spp.)

Genome‐wide association study of multiple yield traits in a diversity panel of polyploid sugarcane (Saccharum spp.)

Genome-wide association study of multiple yield components in a diversity panel of polyploid sugarcane (Saccharum spp.)

Genome-wide association study revealed loci linked to post-drought recovery and traits related to persistence of smooth bromegrass (Bromus inermis)

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