Development and validation of cross-transferable and polymorphic DNA markers for detecting alien genome introgression in Oryza sativa from Oryza brachyantha.
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.
National Rice Research Institute, Cuttack, 753006, Odisha, India.
Soham
S
Ray
National Rice Research Institute, Cuttack, 753006, Odisha, India.
Lotan K
LK
Bose
National Rice Research Institute, Cuttack, 753006, Odisha, India.
Joshitha
J
Ray
National Rice Research Institute, Cuttack, 753006, Odisha, India.
Umakanta
U
Ngangkham
National Rice Research Institute, Cuttack, 753006, Odisha, India.
Jawahar L
JL
Katara
National Rice Research Institute, Cuttack, 753006, Odisha, India.
Sanghamitra
S
Samantaray
National Rice Research Institute, Cuttack, 753006, Odisha, India.
Lambodar
L
Behera
National Rice Research Institute, Cuttack, 753006, Odisha, India.
Mahender
M
Anumalla
National Rice Research Institute, Cuttack, 753006, Odisha, India.
Onkar N
ON
Singh
State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, Beijing, 100101, China.
Meingsheng
M
Chen
Arizona Genomics Institute, School of Plant Sciences, BIO5 Institute, University of Arizona, Tucson, AZ, 85721, USA.
Rod A
RA
Wing
National Rice Research Institute, Cuttack, 753006, Odisha, India. tmnrcpb@gmail.com.
Trilochan
T
Mohapatra
D002874:Chromosome Mapping; D003433:Crosses, Genetic; D017931:DNA Primers / Q000235:genetics*; D018744:DNA, Plant / Q000235:genetics*; D060467:Disease Resistance; D020224:Expressed Sequence Tags; D005819:Genetic Markers; D018745:Genome, Plant; D018895:Microsatellite Repeats; D012275:Oryza / Q000235:genetics*; D011110:Polymorphism, Genetic; D015203:Reproducibility of Results
D017931:DNA Primers; D018744:DNA, Plant; D005819:Genetic Markers
Cleaved amplified polymorphic sequence (CAPS); Cross-transferable co-dominant molecular markers; Monosomic alien addition line (MAAL); Oryza brachyantha; Oryza sativa; Relative gene enrichment index (RGEI); Sequence tagged microsatellite (STMS); Sequence tagged sites (STS); Simple sequence repeats (SSR); Whole genome sequence (WGS)