Genomic Comparison and Population Diversity Analysis Provide Insights into the Domestication and Improvement of Flax

Zhang, Jianping; Qi, Yanni; Wang, Limin; Wang, Lili; Yan, Xin; Dang, Zhao; Li, Wenjuan; Zhao, Wei; Pei, Xinwu; Li, Xuming; Liu, Min; Tan, Mingqian; Wang, Lei; Long, Yan; Wang, Jing; Zhang, Xuewen; ZhanHai, Dang; Zheng, Hongkun; Liu, Touming

doi:10.1016/j.isci.2020.100967

Cited by 43 publications

(57 citation statements)

References 90 publications

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“…, 2019; Zhang et al. , 2020a,b), which provides opportunities for exploring bast fiber formation and evolution in these crops.…”

Section: Introductionmentioning

confidence: 99%

Genomic analyses provide comprehensive insights into the domestication of bast fiber crop ramie (Boehmeria nivea)

Wang

et al. 2021

The Plant Journal

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SUMMARY Ramie (Boehmeria nivea) is an economically important natural fiber‐producing crop that has been cultivated for thousands of years in China; however, the evolution of this crop remains largely unknown. Here, we report a ramie domestication analysis based on genome assembly and resequencing of cultivated and wild accessions. Two chromosome‐level genomes representing wild and cultivated ramie were assembled de novo. Numerous structural variations between two assemblies, together with the genetic variations from population resequencing, constituted a comprehensive genomic variation map for ramie. Domestication analysis identified 71 high‐confidence selective sweeps comprising 320 predicted genes, and 29 genes from sweeps were associated with fiber growth in the expression. In addition, we identified seven genetic loci associated with the fiber yield trait in the segregated population derived from the crossing of two assembled accessions, and two of which showed an overlap with the selective sweeps. These findings indicated that bast fiber traits were focused on during the domestication history of ramie. This study sheds light on the domestication of ramie and provides a valuable resource for biological and breeding studies of this important crop.

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“…, 2019; Zhang et al. , 2020a,b), which provides opportunities for exploring bast fiber formation and evolution in these crops.…”

Section: Introductionmentioning

confidence: 99%

Genomic analyses provide comprehensive insights into the domestication of bast fiber crop ramie (Boehmeria nivea)

Wang

et al. 2021

The Plant Journal

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“…The PacBio Iso-Seq technique determined that each gene contains 7.4 exons on average, which is 1.7 times that of the reference genome (Figure 1(C)). Flax is an important economic crop, and the findings that have been published about flax genome sequencing have helped to promote basic research about flax plants [35,36]. In the present study, Iso-Seq sequencing technology was used to produce 20.34 Gb of clean data from eight cells, and a total of 113,471 consensus transcript sequences were obtained.…”

Section: Resultsmentioning

confidence: 99%

Full-length tran sequencing provides insight into lignan and lignin metabolism relation

Xie

Dai

Sun

et al. 2020

Biotechnology & Biotechnological Equipment

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Flax (Linum usitatissimum L.) is an important economic crop worldwide. The lignin content of flax stems directly determines the quality of flax fiber, and excessively high lignin content in the fiber leads to pollutant discharge by the textile industry. Flax seeds also contain lignans, a group of compounds that are structurally similar to lignin and highly beneficial for human health. The biosynthesis of lignan and lignin occurs in the same metabolic pathway. To elucidate the metabolic relationship between these two compounds and the regulatory nodes of their metabolic processes, third generation (Iso-Seq) and second generation (Illumina) sequencing technologies were used in this study to obtain the transcriptomes of a pair of flax cultivars with significant differences in lignan content. The results showed that the differentially expressed genes (DEGs) are significantly enriched in the lignin and lignan biosynthesis pathways. Ten genes with significant differences in expression (jLog2 FCj>4) were selected for quantitative real-time polymerase chain reaction (qRT-PCR) analysis. The expression levels of these genes all were significantly different in Shuangya 4 and NEW at different stages of flax seed and stem development. We speculated that these genes were most likely closely related to the lignan and lignin metabolism. We also found that the lignan and lignin content are significantly negatively correlated with each other during flax seed and stem development. The findings of this study provide a scientific basis for the application of biotechnological methods to the development of new high-quality flax cultivars with high lignan and low lignin content.

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“…To test the hypothesis that the diversity of imprinted genes are different in flax population, we collated all SNPs (3,191 SNPs) of 241 imprinted genes and compared the nucleotide diversity between oil flax (78 germplasms) and fiber flax subgroups (51 germplasms) which represented two primary morphotypes of cultivated flax (Zhang et al ., 2020). The π values of all imprinted genes, MEGs or PEGs decreased significantly in fiber flax compared with oil flax ( P < 0.0001, t test) (Figure 6A-C).…”

Section: Resultsmentioning

confidence: 99%

“…Cultivated flax were domesticated from a pale flax ( Linum bienne ) for oil usage at 10,000 years ago in the Near East and differentiated into fiber, OF and oil subgroups during the domestication of flax (Guo et al ., 2020; Allaby et al ., 2005; Fu and Allaby, 2010). Some genes underlying important traits including plant architecture, flowering, dehiscence, oil production and yield underwent strong artificial selection in the domestication process of flax (Guo et al ., 2020; Zhang et al ., 2020). Whether imprinted genes are also undergone artificial selection during flax domestication has not been reported.…”

Section: Introductionmentioning

confidence: 99%

Genome-wide screen of genomic imprinting in endosperm and population-level analysis reveal allelic variation for imprinting in flax

Jiang

Guo

et al. 2020

Preprint

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Genomic imprinting is an epigenetic phenomenon caused by the biased expression of maternally and paternally inherited alleles. In flowering plants, genomic imprinting predominantly occurs in triploid endosperm and plays a vital role in seed development. In this study, we identified 241 candidate imprinted genes including 143 maternally expressed imprinted genes (MEGs) and 98 paternally expressed imprinted genes (PEGs) in flax (Linum usitatissimum L.) endosperm using deep RNA sequencing. The conservation of imprinting in plants is very limited and imprinting clustering is not a general feature. MEGs tends to be endosperm expression specific, while PEGs are non-tissue specific. Imprinted SNPs differentiated 200 flax cultivars into oil flax, oil-fiber dual purpose flax (OF) and fiber flax subgroups, suggesting that genomic imprinting contributes to intraspecific variation in flax. The nucleotide diversity (π) of imprinted genes in oil flax subgroup is significantly higher than that in fiber flax subgroup, indicating that some imprinted genes undergo positive selection during flax domestication from oil flax to fiber flax. Imprinted genes undergo positive selection is related to the functions. Eleven imprinted genes related to seed size and weight were identified using the candidate gene-based association study. Our study provides information for further exploring the function and genomic variation of imprinted genes in flax population.

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Genomic Comparison and Population Diversity Analysis Provide Insights into the Domestication and Improvement of Flax

Cited by 43 publications

References 90 publications

Genomic analyses provide comprehensive insights into the domestication of bast fiber crop ramie (Boehmeria nivea)

Genomic analyses provide comprehensive insights into the domestication of bast fiber crop ramie (Boehmeria nivea)

Full-length tran sequencing provides insight into lignan and lignin metabolism relation

Genome-wide screen of genomic imprinting in endosperm and population-level analysis reveal allelic variation for imprinting in flax

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