The Rice Diversity Panel 1 (RDP1) is a resource for genome‐wide association (GWA) studies to explore the five major rice (Oryza sativa L.) subpopulations indica, aus, aromatic, temperate japonica, and tropical japonica (TRJ). Previously collected phenotype data for yield‐related traits in RDP1 were reanalyzed using a recently released 4.8 million single nucleotide polymorphism (SNP) dataset to enhance GWA mapping precision. GWA mapping revealed numerous GWA quantitative trait loci (QTLs) that were specific to one or more subpopulations. Most southern US cultivars are classified tropical japonica (TRJ) or TRJ admixtures, thus TRJ was the focus for validating Rice Diversity Panel 1 GWA QTLs. Two diverse TRJ accessions, L‐202 originating from California, USA, and Trembese from Indonesia, were selected for developing a recombinant inbred line (RIL) population. This RIL population was phenotyped for 20 yield component traits, 16 of which were measured in RDP1, including six agronomic, six panicle architecture, and four seed traits. Genotyping with 1439 polymorphic markers and QTL mapping revealed 43 RIL QTLs. Examination of the GWA QTLs identified 163 GWA QTLs for the same or related traits co‐located with 37 RIL QTLs. A significant overlap was on chromosome 7 (21.8–25.4; 26.8–29.6 Mb) where the well‐known yield related genes, GRAIN WEIGHT7 (GW7) and FRIZZY PANICLE (FZP), respectively, are located and specific to TRJ. In this region, 10 RIL QTLs were co‐located with 36 GWA QTLs for panicle architecture or seed traits, especially secondary branching to increase the number of seeds. RIL QTLs co‐located with GWA QTLs are targets for developing SNP markers that can be utilized in cultivar development.
Sp/Pl Number of spikelets/panicle Sd/Pl Number of seeds/panicle chr. Chromosome cM CentiMorgan
The secondary palate forms from two lateral primordia called the palatal shelves which form a contact in the midline, become adherent at the fusing interface (medial edge epithelia, MEE) and subsequently fuse. The gene encoding transforming growth factor-ß3 (Tgfb3) is strongly and specifically expressed in MEE cells. Our previous study suggested that Tgfb3 expression is controlled via upstream cis-regulatory elements in and around the neighboring Ift43 gene. Another study suggested that the canonical Wnt signaling via ß-Catenin is responsible for the MEE-specific Tgfb3 gene expression, since deletion of the Ctnnb1 gene by a commonly used Keratin 14-Cre (K14Cre) mouse line almost completely abolished Tgfb3 expression in the MEE resulting in cleft palate. Here, we wanted to analyze whether Tcf/Lef consensus binding sites located in the previously identified regions of the Ift43 gene are responsible for the spatiotemporal control of Tgfb3 expression during palatogenesis. We show that contrary to the previous report, deletion of the Ctnnb1 gene in basal MEE cells by the K14Cre driver (the same K14Cre mouse line was used as in the previous study referenced above) does not affect the MEE-specific Tgfb3 expression or TGFß3-dependent palatal epithelial fusion. All mutant embryos showed a lack of palatal rugae accompanied by other craniofacial defects, e.g., a narrow snout and a small upper lip, while only a small subset (<5%) of Ctnnb1 mutants displayed a cleft palate. Moreover, the K14Cre:Ctnnb1 embryos showed reduced levels and altered patterns of Shh expression. Our present data imply that epithelial ß-catenin may not be required for MEE-specific Tgfb3 expression or palatal epithelial fusion.
Grain yield is a quantitative trait that is determined by several agronomic traits. Unfortunately, there is little information about the genetics behind yield components in U.S. rice cultivars. The objective of the study were to 1) conduct a QTL study for identification of chromosome regions associated with yield traits in two US developed rice cultivars and 2) identify candidate genes in major QTL regions related to yield traits. Four rice cultivars were evaluated in the summer 2017 at the University of Arkansas System Division of Agriculture’s Rice Research and Extension Center (RREC) at Stuttgart, AR for 15 agronomic traits associated with yield. Of the four cultivars, “LaGrue” had a higher number of seeds/panicle, number of primary panicle branches/panicle, and number of seeds/plant and “Lemont”, despite having longer panicles and higher 100 seed weight/panicle, produced the least number of seeds among the cultivars. A bi-parental population was developed from a cross between LaGrue and Lemont for QTL analysis. Leaf samples from F2 plants were collected for genetic analysis. A set of 322 F2:3 lines were evaluated in a randomized complete block design (RCBD) for several agronomic traits at two locations with three replications for each line. A total of 17 major QTLs were detected including two major QTLs for plant height on chromosome 1 and two major QTLs for flag leaf length and panicle length on chromosome 8 with seven candidate genes found in these regions. The results from the study would be useful for marker assisted selection in rice breeding.
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