Abstract
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 have 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 to 277 bp, with 1–15 bp accounting for the highest rate (95.55%). The most common InDels were in the form of a single nucleotide (8840), dinucleotide (3700), and trinucleotide (1349), and Ch2 (1505) showed the highest number of InDels among flax chromosomes, while Ch10 (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 analysis (PCA) divided 69 flax accessions into two categories, namely oilseed flax and fibre flax using thirty-two 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 and 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 accessions 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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This research was funded by National Natural Science Foundation of China (31771852 and 31771853) and Special college-level overall planning project for basic scientific research business expenses of Chinese Academy of Agricultural Sciences (Y2019XK15-06).
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AC designed experiment and provided resources. HJ performed experiment, analysed data and wrote original draft. GP designed experiment, analysed data and edited article. TL designed experiment. LC and SH edited artical. HT investigated data of traits. YG provide resources. YW and JT performed part of experiment.
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Supplementary Table S1.
Information of 69 flax accessions used for InDel genotyping. Table S2 Characteristics of 17,110 InDels between 84-3 and 87-3. Table S3 Characteristics of 90 InDel markers used for genetic diversity analysis. Table S4 Statistics of bands amplified by InDel primers. Fig. S1 Distribution of InDel repeats of single nucleotide (a), dinucleotide (b) and trinucleotide (c). Fig. S2 Amplification products in 87-3 and 84-3 with InDel-1—InDel-24 (a), InDel-49—InDel-72 (b) and InDel-73—InDel-90 (c); M, 2000bp marker; 1, 87-3; 2, 84-3. Fig. S3 Amplification products of 69 flax accessions using InDel-14 (a), InDel-40 (b) and InDel-74 (c). M, 2000bp marker; 1 and 2 represent 87-3 and 84-3 respectively; 3-38, flax accessions for oil; 39-69, flax accessions for fibre. (RAR 10373 kb)
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Jiang, H., Pan, G., Liu, T. et al. Development and application of novel InDel markers in flax (Linum usitatissimum L.) through whole-genome re-sequencing. Genet Resour Crop Evol 69, 1471–1483 (2022). https://doi.org/10.1007/s10722-021-01313-2
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DOI: https://doi.org/10.1007/s10722-021-01313-2