Development of Novel SSR Markers for Flax (Linum usitatissimum L.) Using Reduced-Representation Genome Sequencing

Wu, Jianrong; Zhao, Qian; Wu, Guangwen; Zhang, Shuquan; Jiang, Tongmin

doi:10.3389/fpls.2016.02018

Cited by 27 publications

(26 citation statements)

References 42 publications

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“…RNA-Seq data demonstrated that three genes were enriched after ABA treatment and seven after the application of diniconazole. Similar results have been previously observed in Dendrobium officinale 52 and Poa pratensis 53 exposed to abiotic stress conditions. These results indicate that WR04-6 can respond to ABA by actively regulating glycolysis and TCA cycle pathway-related genes and enzyme activities.…”

Section: Discussionsupporting

confidence: 91%

Comparative transcriptomic and physiological analyses of weedy rice and cultivated rice to identify vital differentially expressed genes and pathways regulating the ABA response

Lang

Zeng

et al. 2021

Sci Rep

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Weedy rice is a valuable germplasm resource characterized by its high tolerance to both abiotic and biotic stresses. Abscisic acid (ABA) serves as a regulatory signal in plant cells as part of their adaptive response to stress. However, a global understanding of the response of weedy rice to ABA remains to be elucidated. In the present study, the sensitivity to ABA of weedy rice (WR04-6) was compared with that of temperate japonica Shennong9816 (SN9816) in terms of seed germination and post-germination growth via the application of exogenous ABA and diniconazole, an inhibitor of ABA catabolism. Physiological analysis and a transcriptomic comparison allowed elucidation of the molecular and physiological mechanisms associated with continuous ABA and diniconazole treatment. WR04-6 was found to display higher ABA sensitivity than SN9816, resulting in the rapid promotion of antioxidant enzyme activity. Comparative transcriptomic analyses indicated that the number of differentially expressed genes (DEGs) in WR04-6 seedlings treated with 2 μM ABA or 10 μM diniconazole was greater than that in SN9816 seedlings. Genes involved in stress defense, hormone signal transduction, and glycolytic and citrate cycle pathways were highly expressed in WR04-6 in response to ABA and diniconazole. These findings provide new insight into key processes mediating the ABA response between weedy and cultivated rice.

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Section: Discussionsupporting

confidence: 91%

Comparative transcriptomic and physiological analyses of weedy rice and cultivated rice to identify vital differentially expressed genes and pathways regulating the ABA response

Lang

Zeng

et al. 2021

Sci Rep

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“…The polymorphism rate was 40.70%, which was lower than that of pepper (67.4%) [28], cucumber (54.81%) [34], and Brassica rapa (77%) [26]. Additionally, the PIC obtained was low (0.3097), which was consistent with the results reported by previous studies [10,13,14]. This indicated that InDel was more suitable for the identi cation of ax germplasm resources, since the degree of variation of ax genes was not substantial and the genetic background was narrow.…”

Section: Discussionsupporting

confidence: 89%

“…(1,651,856) [28], the number of InDels detected in this study was low but was higher than that of cucumber (Cucumis sativus) (10,470) [34] and sesame (Sesamum indicum L.) (7,477) [37]. Compared with other markers in ax, the number of InDels was less than that of SNPs [16,19] and more than most SSR markers [8,10,13,43]. The main reason for obtaining such results may be attributed to the fact that compared with the complicated operations of RAPD, AFLP, and SSR, the use of a re-sequencing technology can aid an easy detection and obtainment of a larger number and higher quality of SNPs and InDels in the whole genome.…”

Section: Discussionmentioning

confidence: 86%

Development and Application of Novel InDel Markers in Flax (Linum usitatissimum L.) Through Whole-Genome Re-Sequencing

Jiang

Pan

Liu

et al. 2021

Preprint

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Flax is an important oil and fibre crop grown in Northern Europe, Canada, India, and China. The development of molecular markers has accelerated the process of flax molecular breeding and has improved yield and quality. Presently, simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers in the whole genome have been developed for flax. However, the development of flax insertion/deletion (InDel) markers has not been reported. A total of 17,110 InDel markers were identified by comparing whole-genome re-sequencing data of two accessions (87 − 3 and 84 − 3) with the flax reference genome. The length of InDels ranged from 1–277 bp, with 1–15 bp accounting for the highest rate (95.55%). The most common InDels were in the form of single nucleotide (8840), dinucleotide (3700), and trinucleotide (1349), and chromosome 2 (1505) showed the highest number of InDels among flax chromosomes, while chromosome 10 (913) presented with the lowest number. From 17,110 InDel markers, 90 primers that were evenly distributed in the flax genome were selected. Thirty-two pairs of polymorphic primers were detected in two flax accessions, and the polymorphism rate was 40.70%. Furthermore, genetic diversity analysis, population structure and principal component analyse (PCA) divided 69 flax accessions into two categories, namely oilseed flax and fibre flax using 32 pairs of polymorphic primers. Additionally, correlation analysis showed that InDel-26 and InDel-81 were associated with oil content traits, and two candidate genes (lus10031535 and lus10025284) tightly linked to InDel-26 or InDel-81, might be involved in flax lipid biosynthesis and lipid metabolism. This study is the first to develop InDel markers based on re-sequencing in flax and clustered the markers into two well-separated groups for oil and fibre. The results demonstrated that InDel markers developed herein could be used for flax germplasm identification, genetic diversity analysis, and molecular marker-assisted breeding.

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“…Due to its relatively higher density, excellent consistency, effectiveness, and lower cost when compared with traditional methods, this method has become a popular genotyping method. Indeed, in our previous study SLAF-seq technology was used to develop numerous novel SSRs in flax (Wu et al, 2017 ). Subsequently, in this work sequencing results provided a large quantity of SLAF markers to further drive flax genomic research.…”

Section: Discussionmentioning

confidence: 99%

QTL Mapping of Fiber-Related Traits Based on a High-Density Genetic Map in Flax (Linum usitatissimum L.)

Zhao

Zhang

et al. 2018

Front. Plant Sci.

Self Cite

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A genetic map is an important and valuable tool for quantitative trait locus (QTL) mapping, marker-assisted selection (MAS)-based breeding, and reference-assisted chromosome assembly. In this study, 112 F2 plants from a cross between Linum usitatissimum L. “DIANE” and “NY17” and parent plants were subjected to high-throughput sequencing and specific-locus amplified fragment (SLAF) library construction. After preprocessing, 61.64 Gb of raw data containing 253.71 Mb paired-end reads, each 101 bp in length, were obtained. A total of 192,797 SLAFs were identified, of which 23,115 were polymorphic, with a polymorphism rate of 11.99%. Finally, 2,339 SLAFs were organized into a linkage map consisting of 15 linkage groups (LGs). The total length of the genetic map was 1483.25 centimorgans (cM) and the average distance between adjacent markers was 0.63 cM. Combined with flax chromosome-scale pseudomolecules, 12 QTLs associating with 6 flax fiber-related traits were mapped on the chromosomal scaffolds. This high-density genetic map of flax should serve as a foundation for flax fine QTL mapping, draft genome assembly, and MAS-guided breeding. Ultimately, the genomic regions identified in this research could potentially be valuable for improving flax fiber cultivars, as well as for identification of candidate genes involved in flax fiber formation processes.Significance statementA high-density genetic map of flax was constructed, and QTLs were identified on the sequence scaffolds to be interrelated with fiber-related traits. The results of this study will not only provide a platform for gene/QTL fine mapping, map-based gene isolation, and molecular breeding for flax, but also provide a reference to help position sequence scaffolds on the physical map and assist in the process of assembling the flax genome sequence.

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Development of Novel SSR Markers for Flax (Linum usitatissimum L.) Using Reduced-Representation Genome Sequencing

Cited by 27 publications

References 42 publications

Comparative transcriptomic and physiological analyses of weedy rice and cultivated rice to identify vital differentially expressed genes and pathways regulating the ABA response

Comparative transcriptomic and physiological analyses of weedy rice and cultivated rice to identify vital differentially expressed genes and pathways regulating the ABA response

Development and Application of Novel InDel Markers in Flax (Linum usitatissimum L.) Through Whole-Genome Re-Sequencing

QTL Mapping of Fiber-Related Traits Based on a High-Density Genetic Map in Flax (Linum usitatissimum L.)

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