Identification of genic SSRs and construction of a SSR-based linkage map in Brassica juncea
Search for genic SSRs from transcriptome sequence data of Brassica juncea and B. nigra and from unigene databank of B. rapa resulted in identification of 20,529 SSRs from 330,827 gene sequences. Identified SSRs (named as unigene microsatellite; UGM) were characterized based on their number of repeat...
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Published in | Euphytica Vol. 213; no. 1; p. 1 |
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Main Authors | , , , , , |
Format | Journal Article |
Language | English |
Published |
Dordrecht
Springer Netherlands
2017
Springer Springer Nature B.V |
Subjects | |
Online Access | Get full text |
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Summary: | Search for genic SSRs from transcriptome sequence data of
Brassica juncea
and
B. nigra
and from unigene databank of
B. rapa
resulted in identification of 20,529 SSRs from 330,827 gene sequences. Identified SSRs (named as unigene microsatellite; UGM) were characterized based on their number of repeats, type of motif and base composition. Primers were designed for 2118 UGMs after in silico polymorphism survey and were tested across 11 different genotypes of
B. juncea
and
B. rapa
for PCR amplification and polymorphism. It resulted in clear-cut amplification from 1993 UGMs of which 1319 UGMs showed polymorphism. It was observed that a priori in silico polymorphism survey helped in increasing the polymorphism percentage (6.1–13.2) by PCR amplification. We also report here the development of first SSR-based linkage map of
Brassica juncea
using a DH mapping population derived from F
1
of the cross between the lines EH-2 and Pusajaikisan. The map consisted of 860 markers comprising 462 UGMs, 157 BAC-derived SSRs and 241 intron polymorphic markers and covered a total genetic length of 2073.6 cM. The study also reports an interesting observation of appearance of novel non-parental bands in the mapping population from 18 SSRs and 13 IP markers. Search of
Arabidopsis
genes orthologous to their primer sequences showed that 11 of such
Arabidopsis
genes code for proteins involved in various abiotic stresses. The highly transferable genic SSRs developed in the study would serve as valuable resources for comparative genome mapping, mapping of qualitative and quantitative traits, gene cloning and marker-assisted breeding in
Brassica
species. |
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ISSN: | 0014-2336 1573-5060 |
DOI: | 10.1007/s10681-016-1814-z |