TY - JOUR
T1 - Development and validation of cross-transferable and polymorphic DNA markers for detecting alien genome introgression in Oryza sativa from Oryza brachyantha
AU - Ray, Soham
AU - Bose, Lotan K.
AU - Ray, Joshitha
AU - Ngangkham, Umakanta
AU - Katara, Jawahar L.
AU - Samantaray, Sanghamitra
AU - Behera, Lambodar
AU - Anumalla, Mahender
AU - Singh, Onkar N.
AU - Chen, Meingsheng
AU - Wing, Rod A.
AU - Mohapatra, Trilochan
N1 - Publisher Copyright:
© 2016, Springer-Verlag Berlin Heidelberg.
PY - 2016/8/1
Y1 - 2016/8/1
N2 - African wild rice Oryza brachyantha (FF), a distant relative of cultivated rice Oryza sativa (AA), carries genes for pests and disease resistance. Molecular marker assisted alien gene introgression from this wild species to its domesticated counterpart is largely impeded due to the scarce availability of cross-transferable and polymorphic molecular markers that can clearly distinguish these two species. Availability of the whole genome sequence (WGS) of both the species provides a unique opportunity to develop markers, which are cross-transferable. We observed poor cross-transferability (~0.75 %) of O. sativa specific sequence tagged microsatellite (STMS) markers to O. brachyantha. By utilizing the genome sequence information, we developed a set of 45 low cost PCR based co-dominant polymorphic markers (STS and CAPS). These markers were found cross-transferrable (84.78 %) between the two species and could distinguish them from each other and thus allowed tracing alien genome introgression. Finally, we validated a Monosomic Alien Addition Line (MAAL) carrying chromosome 1 of O. brachyantha in O. sativa background using these markers, as a proof of concept. Hence, in this study, we have identified a set molecular marker (comprising of STMS, STS and CAPS) that are capable of detecting alien genome introgression from O. brachyantha to O. sativa.
AB - African wild rice Oryza brachyantha (FF), a distant relative of cultivated rice Oryza sativa (AA), carries genes for pests and disease resistance. Molecular marker assisted alien gene introgression from this wild species to its domesticated counterpart is largely impeded due to the scarce availability of cross-transferable and polymorphic molecular markers that can clearly distinguish these two species. Availability of the whole genome sequence (WGS) of both the species provides a unique opportunity to develop markers, which are cross-transferable. We observed poor cross-transferability (~0.75 %) of O. sativa specific sequence tagged microsatellite (STMS) markers to O. brachyantha. By utilizing the genome sequence information, we developed a set of 45 low cost PCR based co-dominant polymorphic markers (STS and CAPS). These markers were found cross-transferrable (84.78 %) between the two species and could distinguish them from each other and thus allowed tracing alien genome introgression. Finally, we validated a Monosomic Alien Addition Line (MAAL) carrying chromosome 1 of O. brachyantha in O. sativa background using these markers, as a proof of concept. Hence, in this study, we have identified a set molecular marker (comprising of STMS, STS and CAPS) that are capable of detecting alien genome introgression from O. brachyantha to O. sativa.
KW - Cleaved amplified polymorphic sequence (CAPS)
KW - Cross-transferable co-dominant molecular markers
KW - Monosomic alien addition line (MAAL)
KW - Oryza brachyantha
KW - Oryza sativa
KW - Relative gene enrichment index (RGEI)
KW - Sequence tagged microsatellite (STMS)
KW - Sequence tagged sites (STS)
KW - Simple sequence repeats (SSR)
KW - Whole genome sequence (WGS)
UR - http://www.scopus.com/inward/record.url?scp=84974853841&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=84974853841&partnerID=8YFLogxK
U2 - 10.1007/s00438-016-1214-z
DO - 10.1007/s00438-016-1214-z
M3 - Article
C2 - 27299359
AN - SCOPUS:84974853841
SN - 1617-4615
VL - 291
SP - 1783
EP - 1794
JO - Molecular Genetics and Genomics
JF - Molecular Genetics and Genomics
IS - 4
ER -