Assessment of FAE1 polymorphisms in three Brassica species using EcoTILLING and their association with differences in seed erucic acid contents

Wang, Nian; Shi, Lei; Tian, Fang; Ning, Huicai; Wu, Xiaoming; Long, Yan; Meng, Jinling

doi:10.1186/1471-2229-10-137

Cited by 63 publications

(51 citation statements)

References 36 publications

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“…They can be more numerous than other types of markers, but this is difficult to test. Before next generation sequencing (NGS) technique was developed, a number of other platforms were available for their identification, such as SNP Gene-Chip [19], high-resolution melt (HRM) analysis [20], TILLING and EcoTILLING [21,22]. With the improved sequencing technology, the last two years have seen the development of NGS combining restriction-site associated DNA (RAD) for SNP testing [23].…”

Section: Introductionmentioning

confidence: 99%

Construction of a high-density genetic map for grape using next generation restriction-site associated DNA sequencing

et al. 2012

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BackgroundGenetic mapping and QTL detection are powerful methodologies in plant improvement and breeding. Construction of a high-density and high-quality genetic map would be of great benefit in the production of superior grapes to meet human demand. High throughput and low cost of the recently developed next generation sequencing (NGS) technology have resulted in its wide application in genome research. Sequencing restriction-site associated DNA (RAD) might be an efficient strategy to simplify genotyping. Combining NGS with RAD has proven to be powerful for single nucleotide polymorphism (SNP) marker development.ResultsAn F1 population of 100 individual plants was developed. In-silico digestion-site prediction was used to select an appropriate restriction enzyme for construction of a RAD sequencing library. Next generation RAD sequencing was applied to genotype the F1 population and its parents. Applying a cluster strategy for SNP modulation, a total of 1,814 high-quality SNP markers were developed: 1,121 of these were mapped to the female genetic map, 759 to the male map, and 1,646 to the integrated map. A comparison of the genetic maps to the published Vitis vinifera genome revealed both conservation and variations.ConclusionsThe applicability of next generation RAD sequencing for genotyping a grape F1 population was demonstrated, leading to the successful development of a genetic map with high density and quality using our designed SNP markers. Detailed analysis revealed that this newly developed genetic map can be used for a variety of genome investigations, such as QTL detection, sequence assembly and genome comparison.

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Section: Introductionmentioning

confidence: 99%

Construction of a high-density genetic map for grape using next generation restriction-site associated DNA sequencing

et al. 2012

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“…In the case of poplar ( Populus trichocarpa ), EcoTILLING identified 63 SNPs in nine different genes in 41 different populations [15]. In brief, several reports have indicated that EcoTILLING is an accurate, high-throughput and low-cost technique for the discovery and evaluation of nucleotide variations in candidate genes associated with target traits [16]–[18]. Recently, association analysis emerged as a powerful approach to identify the role of genetic polymorphism in phenotypic variations in response to environmental stresses [19], [20].…”

Section: Introductionmentioning

confidence: 99%

Single Nucleotide Polymorphisms in HSP17.8 and Their Association with Agronomic Traits in Barley

Xia

Zheng-xiang

et al. 2013

PLoS ONE

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Small heat shock protein 17.8 (HSP17.8) is produced abundantly in plant cells under heat and other stress conditions and may play an important role in plant tolerance to stress environments. However, HSP17.8 may be differentially expressed in different accessions of a crop species exposed to identical stress conditions. The ability of different genotypes to adapt to various stress conditions resides in their genetic diversity. Allelic variations are the most common forms of genetic variation in natural populations. In this study, single nucleotide polymorphisms (SNPs) of the HSP17.8 gene were investigated across 210 barley accessions collected from 30 countries using EcoTILLING technology. Eleven SNPs including 10 from the coding region of HSP17.8 were detected, which form nine distinguishable haplotypes in the barley collection. Among the 10 SNPs in the coding region, six are missense mutations and four are synonymous nucleotide changes. Five of the six missense changes are predicted to be deleterious to HSP17.8 function. The accessions from Middle East Asia showed the higher nucleotide diversity of HSP17.8 than those from other regions and wild barley (H. spontaneum) accessions exhibited greater diversity than the cultivated barley (H. vulgare) accessions. Four SNPs in HSP17.8 were found associated with at least one of the agronomic traits evaluated except for spike length, namely number of grains per spike, thousand kernel weight, plant height, flag leaf area and leaf color. The association between SNP and these agronomic traits may provide new insight for study of the gene's potential contribution to drought tolerance of barley.

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“…In all modern oilseed rape low-erucic acid accessions, the reduction in cytosolic fatty acid elongation is considered to be due to the loss of function in a gene homolog to Arabidopsis FATTY ACID ELONGASE1 (Wu et al, 2008;Wang et al, 2010); that is, the elongation process itself seems to be disrupted, not the precursor supply. Our study includes low-and high-erucic acid oilseed rape cultivars.…”

Section: Provision Of Precursors For Cytosolic Elongation Of Fatty Acidsmentioning

confidence: 99%

Quantitative Multilevel Analysis of Central Metabolism in Developing Oilseeds of Oilseed Rape during in Vitro Culture

et al. 2015

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Seeds provide the basis for many food, feed, and fuel products. Continued increases in seed yield, composition, and quality require an improved understanding of how the developing seed converts carbon and nitrogen supplies into storage. Current knowledge of this process is often based on the premise that transcriptional regulation directly translates via enzyme concentration into flux. In an attempt to highlight metabolic control, we explore genotypic differences in carbon partitioning for in vitro cultured developing embryos of oilseed rape (Brassica napus). We determined biomass composition as well as 79 net fluxes, the levels of 77 metabolites, and 26 enzyme activities with specific focus on central metabolism in nine selected germplasm accessions. Overall, we observed a tradeoff between the biomass component fractions of lipid and starch. With increasing lipid content over the spectrum of genotypes, plastidic fatty acid synthesis and glycolytic flux increased concomitantly, while glycolytic intermediates decreased. The lipid/starch tradeoff was not reflected at the proteome level, pointing to the significance of (posttranslational) metabolic control. Enzyme activity/flux and metabolite/flux correlations suggest that plastidic pyruvate kinase exerts flux control and that the lipid/starch tradeoff is most likely mediated by allosteric feedback regulation of phosphofructokinase and ADP-glucose pyrophosphorylase. Quantitative data were also used to calculate in vivo mass action ratios, reaction equilibria, and metabolite turnover times. Compounds like cyclic 39,59-AMP and sucrose-6-phosphate were identified to potentially be involved in so far unknown mechanisms of metabolic control. This study provides a rich source of quantitative data for those studying central metabolism.Seeds develop by absorbing nutrients from their mother plant and using these to synthesize a combination of starch, protein, and lipid. The size and number of seeds that finally develop determine the crop's yield, while their composition determines the end-use quality of the crop. The conversion of nutrients into storage products involves a complex network of metabolic reactions, many of which are subject to transcriptional, translational, and posttranslational regulation. Attempting to engineer seed composition clearly requires a firm understanding of these regulatory networks.The seed's central metabolism differs markedly from those of both a photosynthesizing leaf and a root. In most species, the immature seed is green for a period during its development, so during this phase it is regarded as being photoheterotrophic. A further level of complexity arises as a result of spatial heterogeneity within the seed (Rolletschek et al., 2011; Borisjuk et al.,

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Assessment of FAE1 polymorphisms in three Brassica species using EcoTILLING and their association with differences in seed erucic acid contents

Cited by 63 publications

References 36 publications

Construction of a high-density genetic map for grape using next generation restriction-site associated DNA sequencing

Construction of a high-density genetic map for grape using next generation restriction-site associated DNA sequencing

Single Nucleotide Polymorphisms in HSP17.8 and Their Association with Agronomic Traits in Barley

Quantitative Multilevel Analysis of Central Metabolism in Developing Oilseeds of Oilseed Rape during in Vitro Culture

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