STUDIES ON DEVELOPMENT AND TRANSFERABILITY OF FINGER MILLET SSR MARKERS ACROSS OTHER SMALL MILLETS
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Date
2020-12-15, 2020-12-15
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UNIVERSITY OF AGRICULTURAL SCIENCES, BANGALORE
UNIVERSITY OF AGRICULTURAL SCIENCES, BANGALORE
UNIVERSITY OF AGRICULTURAL SCIENCES, BANGALORE
Abstract
The transcriptome sequence information of finger millet available in NCBI database was in silico mined using Krait software for microsatellite identification and primer development. A total of 677 perfect microsatellites were identified with a relative abundancy of 1288.3 loci/Mb. Among the 677 SSRs identified, mono nucleotide repeats were the most abundant (55.24%), followed by di-(34.27%), tri-(9.45%), penta-(0.74%) and tetra nucleotides (0.3%). Out of 677 EST-SSRs identified, primer pairs were
successfully designed for 446 SSRs and all the primer pairs excluding the mono nucleotide repeats were in silico validated. The annealing temperature and the amplicon size of the in silico validated primers were in the range of 59-63°C and 100-206bp, respectively. In addition, the transferability of 40 finger millet genomic SSRs revealed the highest transferability in sorghum (77.5%) where 31 out of 40 SSRs were amplified, followed by 27 SSRs in barnyard millet (67.5%), 26 in pearl millet (65%), 24 in little millet (60%), 22 in brown top millet (55%), 21 in proso millet (52.5%), 18 in foxtail millet (45%), 17 in rice (42.5%), 15 in kodo millet (37.5%) and 7 in maize (17.5%). Highest transferability of finger millet SSR markers in sorghum indicated high synteny between the closely related species. This study adds new generation of markers to the orphan crops like kodo, proso, brown top and little millet which lack sufficient genomic resources, it also enhances genomic resources in the existing pool in crops like foxtail millet, pearl millet, maize and rice.
The transcriptome sequence information of finger millet available in NCBI database was in silico mined using Krait software for microsatellite identification and primer development. A total of 677 perfect microsatellites were identified with a relative abundancy of 1288.3 loci/Mb. Among the 677 SSRs identified, mono nucleotide repeats were the most abundant (55.24%), followed by di-(34.27%), tri-(9.45%), penta-(0.74%) and tetra nucleotides (0.3%). Out of 677 EST-SSRs identified, primer pairs were successfully designed for 446 SSRs and all the primer pairs excluding the mono nucleotide repeats were in silico validated. The annealing temperature and the amplicon size of the in silico validated primers were in the range of 59-63°C and 100-206bp, respectively. In addition, the transferability of 40 finger millet genomic SSRs revealed the highest transferability in sorghum (77.5%) where 31 out of 40 SSRs were amplified, followed by 27 SSRs in barnyard millet (67.5%), 26 in pearl millet (65%), 24 in little millet (60%), 22 in brown top millet (55%), 21 in proso millet (52.5%), 18 in foxtail millet (45%), 17 in rice (42.5%), 15 in kodo millet (37.5%) and 7 in maize (17.5%). Highest transferability of finger millet SSR markers in sorghum indicated high synteny between the closely related species. This study adds new generation of markers to the orphan crops like kodo, proso, brown top and little millet which lack sufficient genomic resources, it also enhances genomic resources in the existing pool in crops like foxtail millet, pearl millet, maize and rice.
The transcriptome sequence information of finger millet available in NCBI database was in silico mined using Krait software for microsatellite identification and primer development. A total of 677 perfect microsatellites were identified with a relative abundancy of 1288.3 loci/Mb. Among the 677 SSRs identified, mono nucleotide repeats were the most abundant (55.24%), followed by di-(34.27%), tri-(9.45%), penta-(0.74%) and tetra nucleotides (0.3%). Out of 677 EST-SSRs identified, primer pairs were successfully designed for 446 SSRs and all the primer pairs excluding the mono nucleotide repeats were in silico validated. The annealing temperature and the amplicon size of the in silico validated primers were in the range of 59-63°C and 100-206bp, respectively. In addition, the transferability of 40 finger millet genomic SSRs revealed the highest transferability in sorghum (77.5%) where 31 out of 40 SSRs were amplified, followed by 27 SSRs in barnyard millet (67.5%), 26 in pearl millet (65%), 24 in little millet (60%), 22 in brown top millet (55%), 21 in proso millet (52.5%), 18 in foxtail millet (45%), 17 in rice (42.5%), 15 in kodo millet (37.5%) and 7 in maize (17.5%). Highest transferability of finger millet SSR markers in sorghum indicated high synteny between the closely related species. This study adds new generation of markers to the orphan crops like kodo, proso, brown top and little millet which lack sufficient genomic resources, it also enhances genomic resources in the existing pool in crops like foxtail millet, pearl millet, maize and rice.