Variation of OsTZF1 gene related to salt tolerance in Doc Phung rice variety using whole geneome sequencing
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Abstract
In this study, the next generation sequencing technology was used to resequence the geneome of Doc Phung rice varieties (salt-tolerant variety) and Nep Mo (salt-susceptible variety) to identify functional markers that are involved in salt tolerance mechanisms in Doc Phung rice variety. In comparision with the reference geneome, the result showed that Doc Phung geneome was consisted of 1,918,726 variations of SNP and 163.409 InDels (81,435 insertions, and 81,974 deletion). Whereas in Nep Mo variety, there were 1,931,380 SNPs and 171.663 InDels (88,473 insertions and 83,190 deletion). Most of the variants are located in non-functional regions including upstreams, downstream, and intergeneic, accounting for over 75%. The variation of OsTZF1 (LOC_Os05g10670.1) gene that regulates the expression of those gene related to biological and abiotic stress factors, showed that there were 7 SNPs and 9 nucleotides insertion (encode 3 amino acid arginine) in Doc Phung variety when being compared to Nep Mo based on reference geneome. This information will help the breeders to apply as a molecular marker, using salt-tolerant rice breeding program in the future.
Tóm tắt
Trong nghiên cứu này, kỹ thuật giải trình tự thế hệ mới (next generation sequencing) được ứng dụng để giải trình tự của bộ gene 2 giống lúa Đốc Phụng (giống chống chịu mặn) và giống Nếp Mỡ (giống mẫn cảm với mặn), nhằm tìm các chỉ thị phân tử là gene chức năng mà các gene này liên quan đến cơ chế chống chịu mặn có trong giống lúa Đốc Phụng. Kết quả so sánh với bộ gene tham chiếu, bộ gene của giống lúa Đốc Phụng có khoảng 1.918.726 biến thể dạng thay đổi một nucleotide (Single Nucleotide Polymorphism) và và chèn vào khoảng 81.435, mất đi khoảng 81.974. Trong khi đó ở giống Nếp Mỡ, có khoảng 1.931.380 SNP và chèn vào khoảng 88.473, mất đi khoảng 83.190 vùng DNA. Đa số các biến thể xuất hiện ở các vùng không mang chức năng như trước sau và giữa các gene chiếm tỉ lệ trên 75%. Kết quả khảo sát biến thể xuất hiện trong vùng gene OsTZF1 (LOC_Os05g10670.1), có chức năng điều hòa các nhóm gene liên quan đến các yếu tố stress sinh học và phi sinh học, cho thấy ở giống Đốc Phụng có 7 biến thể SNP và có chèn thêm 9 nucleotide mã hóa 3 amino acid arginine khi so với giống Nếp Mỡ dựa trên bộ gene tham chiếu. Thông tin này giúp cho các nhà chọn giống sử dụng nó như chi thị phân tử, chọn tạo giống chống chịu...
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