title: Identification of candidate genes associated with positive and negative heterosis in rice.
abstract: 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 F1 hybrid 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.
authors.affiliation: Dale Bumpers National Rice Research Center (DB NRRC), Agricultural Research Service, United States Department of Agriculture (USDA-ARS), Stuttgart, Arkansas, United States of America; Rice Research and Extension Center, University of Arkansas Division of Agriculture, Stuttgart, Arkansas, United States of America; Department of Plant Pathology, Ohio State University, Columbus, Ohio, United States of America.
authors.forename: R C
authors.initials: RC
authors.lastname: Venu
authors.affiliation: Dale Bumpers National Rice Research Center (DB NRRC), Agricultural Research Service, United States Department of Agriculture (USDA-ARS), Stuttgart, Arkansas, United States of America; Rice Research and Extension Center, University of Arkansas Division of Agriculture, Stuttgart, Arkansas, United States of America.
authors.forename: Jianbing
authors.initials: J
authors.lastname: Ma
authors.affiliation: Dale Bumpers National Rice Research Center (DB NRRC), Agricultural Research Service, United States Department of Agriculture (USDA-ARS), Stuttgart, Arkansas, United States of America.
authors.forename: Yulin
authors.initials: Y
authors.lastname: Jia
authors.affiliation: Dale Bumpers National Rice Research Center (DB NRRC), Agricultural Research Service, United States Department of Agriculture (USDA-ARS), Stuttgart, Arkansas, United States of America; Rice Research and Extension Center, University of Arkansas Division of Agriculture, Stuttgart, Arkansas, United States of America.
authors.forename: Guangjie
authors.initials: G
authors.lastname: Liu
authors.affiliation: Dale Bumpers National Rice Research Center (DB NRRC), Agricultural Research Service, United States Department of Agriculture (USDA-ARS), Stuttgart, Arkansas, United States of America.
authors.forename: Melissa H
authors.initials: MH
authors.lastname: Jia
authors.affiliation: Delaware Biotechnology Institute, University of Delaware, Newark, Delaware, United States of America.
authors.forename: Kan
authors.initials: K
authors.lastname: Nobuta
authors.affiliation: Department of Plant Pathology, Ohio State University, Columbus, Ohio, United States of America.
authors.forename: M V
authors.initials: MV
authors.lastname: Sreerekha
authors.affiliation: Rice Research and Extension Center, University of Arkansas Division of Agriculture, Stuttgart, Arkansas, United States of America.
authors.forename: Karen
authors.initials: K
authors.lastname: Moldenhauer
authors.affiliation: Dale Bumpers National Rice Research Center (DB NRRC), Agricultural Research Service, United States Department of Agriculture (USDA-ARS), Stuttgart, Arkansas, United States of America.
authors.forename: Anna M
authors.initials: AM
authors.lastname: McClung
authors.affiliation: Delaware Biotechnology Institute, University of Delaware, Newark, Delaware, United States of America.
authors.forename: Blake C
authors.initials: BC
authors.lastname: Meyers
authors.affiliation: Department of Plant Pathology, Ohio State University, Columbus, Ohio, United States of America.
authors.forename: Guo-Liang
authors.initials: GL
authors.lastname: Wang
mesh_terms: D002678:Chimera / Q000235:genetics*; D002523:Edible Grain / Q000235:genetics*; D017343:Genes, Plant / Q000502:physiology*; D006823:Hybrid Vigor / Q000502:physiology*; D012275:Oryza / Q000235:genetics*; D010940:Plant Proteins / Q000235:genetics; D019655:Quantitative Trait, Heritable
chemical_list: D010940:Plant Proteins
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