Genetic diversity and genome-wide association analysis in Chinese hulless oat germplasm

Yan, Huihuang; Zhou, Pingping; Peng, Yun; Bekele, Wubishet A.; Ren, Changzhong; Tinker, Nicholas A.; Peng, Yuanying

doi:10.1007/s00122-020-03674-1

Cited by 14 publications

(27 citation statements)

References 62 publications

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“…6d), The long-range LD observed in oat is similar to that in other self-fertilizing species such as wheat 38,39 and barley 40,41 . An association scan detected a strong peak on the end of chromosome 4D, which collocated with the previously reported N1 locus 34,42 (Fig. 6e,f).…”

Section: Resultssupporting

confidence: 88%

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Reference genome assemblies reveal the origin and evolution of allohexaploid oat

et al. 2022

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Common oat (Avena sativa) is an important cereal crop serving as a valuable source of forage and human food. Although reference genomes of many important crops have been generated, such work in oat has lagged behind, primarily owing to its large, repeat-rich polyploid genome. Here, using Oxford Nanopore ultralong sequencing and Hi-C technologies, we have generated a reference-quality genome assembly of hulless common oat, comprising 21 pseudomolecules with a total length of 10.76 Gb and contig N50 of 75.27 Mb. We also produced genome assemblies for diploid and tetraploid Avena ancestors, which enabled the identification of oat subgenomes and provided insights into oat chromosomal evolution. The origin of hexaploid oat is inferred from whole-genome sequencing, chloroplast genomes and transcriptome assemblies of different Avena species. These findings and the high-quality reference genomes presented here will facilitate the full use of crop genetic resources to accelerate oat improvement.

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Section: Resultssupporting

confidence: 88%

“…6c) revealed weak population structure, which is consistent with previous studies [35][36][37] . Most of the hulless landraces were tightly clustered reflecting domestication bottleneck for hulless oat 34 . The LD decay rate was measured as the physical distance at which the average pairwise r 2 dropped to 0.2.…”

Section: Resultsmentioning

confidence: 99%

Reference genome assemblies reveal the origin and evolution of allohexaploid oat

et al. 2022

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“…Its cropped area, however, has rapidly declined during the past decades ( FAOSTATS, 2019 ), even the demand in oat for human consumption has increased in recent years due to its documented health benefits. This is partly attributed to the lower yield of oat compared with that of the other cereal crops ( FAOSTATS, 2019 ; Yan et al, 2020 ). Thus, breeding high-yielding oat varieties are urgently needed to turn oats more competitive and attractive for farmers.…”

Section: Introductionmentioning

confidence: 99%

Position Validation of the Dwarfing Gene Dw6 in Oat (Avena sativa L.) and Its Correlated Effects on Agronomic Traits

Yan

et al. 2021

Front. Plant Sci.

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An F6:8 recombinant inbred line (RIL) population derived from the cross between WAOAT2132 (Dw6) and Caracas along with the two parents were used to evaluate the genetic effects of Dw6 dwarfing gene on plant height and other agronomic traits in oat (Avena sativa L.) across three environments, and develop closely linked markers for marker-assisted selection (MAS) for Dw6. The two parents differed in all investigated agronomic traits except for the number of whorls. The RIL lines showed a bimodal distribution for plant height in all three tested environments, supporting the height of this population was controlled by a single gene. Dw6 significantly reduced plant height (37.66∼44.29%) and panicle length (13.99∼22.10%) but without compromising the coleoptile length which was often positively associated with the reduced stature caused by dwarfing genes. Dw6 has also strong negative effects on hundred kernel weight (14.00∼29.55%), and kernel length (4.21∼9.47%), whereas the effects of Dw6 on the kernel width were not uniform across three environments. By contrast, lines with Dw6 produced more productive tillers (10.11∼10.53%) than lines without Dw6. All these together suggested the potential yield penalty associated with Dw6 might be partially due to the decrease of kernel weight which is attributed largely to the reduction of kernel length. Eighty-one simple sequence repeat (SSR) primer pairs from chromosome 6D were tested, five of them were polymorphic in two parents and in two contrasting bulks, confirming the 6D location of Dw6. By using the five polymorphic markers, Dw6 was mapped to an interval of 1.0 cM flanked by markers SSR83 and SSR120. Caution should be applied in using this information since maker order conflicts were observed. The close linkages of these two markers to Dw6 were further validated in a range of oat lines. The newly developed markers will provide a solid basis for future efforts both in the identification of Dw6 in oat germplasm and in the determination of the nature of the gene through positional cloning.

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“…Genotyping-by-sequencing (GBS), a parallel high-throughput genotyping technique based on sequencing, was developed for complexity reduction in large complex genomes of crops. GBS was utilized for analysis of the genetic diversity, population structure, and genome-wide association study (GWAS) in oat germplasms [3,28,29].…”

Section: Introductionmentioning

confidence: 99%

De Novo Transcriptome Assembly and SNP Discovery for the Development of dCAPS Markers in Oat

et al. 2022

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Cultivated oat (Avena sativa L.) is an important cereal crop that has captured interest worldwide due to its nutritional properties and associated health benefits. Despite this interest, oat has lagged behind other cereal crops in genome studies and the development of DNA markers due to its large and complex genome. RNA-Seq technology has been widely used for transcriptome analysis, functional gene study, and DNA marker development. In this study, we performed the transcriptome sequencing of 10 oat varieties at the seedling stage using the Illumina platform for the development of DNA markers. In total, 31,187,392~41,304,176 trimmed reads (an average of 34,322,925) were generated from 10 oat varieties. All of the trimmed reads of these varieties were assembled and generated, yielding a total of 128,244 assembled unigenes with an average length of 1071.7 bp and N50 of 1752 bp. According to gene ontology (GO) analysis, 30.7% of unigenes were assigned to the “catalytic activity” of the parent term in the molecular function category. Of the 1273 dCAPS markers developed using 491 genotype-specific SNPs, 30 markers exhibiting polymorphism in 28 oat varieties were finally selected. The transcriptome data of oat varieties could be used for functional studies about the seedling stage of oat and information about sequence variations in DNA marker development. These 30 dCAPS markers will be utilized for oat genetic analysis, cultivar identification, and breeders’ rights protection.

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Genetic diversity and genome-wide association analysis in Chinese hulless oat germplasm

Cited by 14 publications

References 62 publications

Reference genome assemblies reveal the origin and evolution of allohexaploid oat

Reference genome assemblies reveal the origin and evolution of allohexaploid oat

Position Validation of the Dwarfing Gene Dw6 in Oat (Avena sativa L.) and Its Correlated Effects on Agronomic Traits

De Novo Transcriptome Assembly and SNP Discovery for the Development of dCAPS Markers in Oat

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