TY - JOUR
T1 - Identification of candidate genes associated with positive and negative heterosis in rice
AU - Venu, R. C.
AU - Ma, Jianbing
AU - Jia, Yulin
AU - Liu, Guangjie
AU - Jia, Melissa H.
AU - Nobuta, Kan
AU - Sreerekha, M. V.
AU - Moldenhauer, Karen
AU - McClung, Anna M.
AU - Meyers, Blake C.
AU - Wang, Guo Liang
N1 - Funding Information:
We thank the staff members of DB NRRC, Stuttgart, AR; Rice Research Unit, Beaumont, TX and, Rice Research and Extension Center, University of Arkansas Division of Agriculture, Stuttgart, AR, Jane Khatenje, Pooja Ghai and Saritha Kontham of Arkansas State University for their help in phenotyping RILs. This work was supported in part by the Plant Genome Research Program of the National Science Foundation [Award numbers: 0701745 and 0321437]. USDA is an equal opportunity provider and employer.
PY - 2014/4/17
Y1 - 2014/4/17
N2 - To identify the genes responsible for yield related traits, and heterosis, massively parallel signature sequencing (MPSS) libraries were constructed from leaves, roots and meristem tissues from the two parents, 'Nipponbare' and '93-11', and their F1 hybrid. From the MPSS libraries, 1-3 million signatures were obtained. Using cluster analysis, commonly and specifically expressed genes in the parents and their F1 hybrid were identified. To understand heterosis in the F1 hybrid, the differentially expressed genes in the F1hybrid were mapped to yield related quantitative trait loci (QTL) regions using a linkage map constructed from 131 polymorphic simple sequence repeat markers with 266 recombinant inbred lines derived from a cross between Nipponbare and 93-11. QTLs were identified for yield related traits including days to heading, plant height, plant type, number of tillers, main panicle length, number of primary branches per main panicle, number of kernels per main panicle, total kernel weight per main panicle, 1000 grain weight and total grain yield per plant. Seventy one QTLs for these traits were mapped, of which 3 QTLs were novel. Many highly expressed chromatin-related genes in the F1 hybrid encoding histone demethylases, histone deacetylases, argonaute-like proteins and polycomb proteins were located in these yield QTL regions. A total of 336 highly expressed transcription factor (TF) genes belonging to 50 TF families were identified in the yield QTL intervals. These findings provide the starting genomic materials to elucidate the molecular basis of yield related traits and heterosis in rice.
AB - To identify the genes responsible for yield related traits, and heterosis, massively parallel signature sequencing (MPSS) libraries were constructed from leaves, roots and meristem tissues from the two parents, 'Nipponbare' and '93-11', and their F1 hybrid. From the MPSS libraries, 1-3 million signatures were obtained. Using cluster analysis, commonly and specifically expressed genes in the parents and their F1 hybrid were identified. To understand heterosis in the F1 hybrid, the differentially expressed genes in the F1hybrid were mapped to yield related quantitative trait loci (QTL) regions using a linkage map constructed from 131 polymorphic simple sequence repeat markers with 266 recombinant inbred lines derived from a cross between Nipponbare and 93-11. QTLs were identified for yield related traits including days to heading, plant height, plant type, number of tillers, main panicle length, number of primary branches per main panicle, number of kernels per main panicle, total kernel weight per main panicle, 1000 grain weight and total grain yield per plant. Seventy one QTLs for these traits were mapped, of which 3 QTLs were novel. Many highly expressed chromatin-related genes in the F1 hybrid encoding histone demethylases, histone deacetylases, argonaute-like proteins and polycomb proteins were located in these yield QTL regions. A total of 336 highly expressed transcription factor (TF) genes belonging to 50 TF families were identified in the yield QTL intervals. These findings provide the starting genomic materials to elucidate the molecular basis of yield related traits and heterosis in rice.
UR - http://www.scopus.com/inward/record.url?scp=84899714676&partnerID=8YFLogxK
U2 - 10.1371/journal.pone.0095178
DO - 10.1371/journal.pone.0095178
M3 - Article
C2 - 24743656
AN - SCOPUS:84899714676
SN - 1932-6203
VL - 9
JO - PloS one
JF - PloS one
IS - 4
M1 - e95178
ER -