The Plant Genome T he semidwarf plant type has been a major focus in rice breeding programs around the world starting with the development of the "Green Revolution" rice variety IR8 by IRRI in 1966 (Chandler, 1972; Khush et al., 2001). IR8 was lodging resistant and responded to nitrogen fertilizer with significant yield increases and a higher harvest index than the best-grown varieties in the 1960s (Chandler, 1972). The yield potential of IR8 was 9 to 10 t ha −1 vs. the yield potential of 6 t ha −1 for the best landraces in the tropical irrigated lowlands in the 1960s (De Datta et al., 1968; Yoshida and Parao, 1972). Much of the yield increase of IR8 was attributed to the semidwarf trait and the ability of the plant to respond to nitrogen fertilizer without lodging (De Datta et al., 1968).
Background: Aroma is an important grain quality trait in rice, controlled by mutations within the BADH2 gene. The trait is simply inherited, and its importance in variety development makes it a practical target for marker-assisted selection in applied breeding programs. The predominant functional mutation within BADH2, an 8-bp indel, can be reliably detected using a PCR-based assay, but the available assays and associated genotyping platforms are insufficient for large-scale applied molecular breeding applications and are not compatible with outsourcing genotyping services. Results: We first characterized SNP diversity across the BADH2 gene in a collection of 2932 rice varieties to determine the number of gene haplotypes in O. sativa. Using 297 gene-based SNPs, 11 haplotype groups were detected, and subsequently identified a minimal set of nine informative SNPs that uniquely identified the BADH2 haplotypes. These nine SNPs were developed into KASP assays and used to examine a panel of 369 U.S. rice accessions. The panel represented modern breeding germplasm and included all known aroma pedigree sources in U.S. rice. Six haplotypes were detected within the U.S. panel, of which two were found in majority (85%) of varieties. A representative set of 39 varieties from all haplotype groups was evaluated phenotypically to distinguish aromatic from non-aromatic lines. Conclusion: One haplotype (Hap 6) was found to be perfectly associated with the aromatic phenotype. A single KASP SNP unique to Hap 6 was demonstrated to reliably differentiate aromatic from non-aromatic rice varieties across U.S. germplasm.
The potential of genomic selection (GS) to increase the efficiency of breeding programs has been clearly demonstrated; however, the implementation of GS in rice (Oryza sativa L.) breeding programs has been limited. In recent years, efforts have begun to work toward implementing GS into the Louisiana State University (LSU) Agricultural Center rice breeding program. One of the first steps for successful GS implementation is to establish a suitable marker set for the target germplasm and a reliable, cost‐effective genotyping platform capable of providing informative marker data with an adequate turnaround time. The objective of this study was to develop a marker set for routine GS and demonstrate its effectiveness in southern U.S. rice germplasm. The utility of the resulting marker set, the LSU500, for GS applications was demonstrated using four years of breeding data across 7,607 experimental lines and four elite biparental populations. The predictive ability of GS ranged from 0.13 to 0.78 for key traits across different market classes and yield trials. Comparisons between phenotypic selection and GS within biparental populations demonstrates similar performance of GS compared with phenotypic selection in predicting future performance. The prediction accuracies obtained with the LSU500 marker set demonstrates the utility of this marker set for cost‐effective GS applications in southern U.S. rice breeding programs. The LSU500 marker set has been established through the genotyping service provider Agriplex Genomics, and in the future, it will undergo improvements to reduce the cost and increase the accuracy of GS.
PVL01' (Reg. no. CV-153, PI 682661), a Provisia (BASF) longgrain rice (Oryza sativa L.) cultivar, was developed by the Louisiana State University Agricultural Center at the H. Rouse Caffey Rice Research Station (HRCRRS) near Crowley, LA, and approved for release by the director of the Louisiana Agricultural Experiment Station in 2017. PVL01 is the first rice cultivar to be released as part of the Provisia Rice System (BASF) with resistance to Provisia herbicide, containing the active ingredient quizalofop, an AACase (group 1) herbicide. PVL01 was derived from the cross 'Cheniere'/BASF1-5 that was made in 2012 at the HRCRRS and advanced in 2014 as an F 2 :F 3 row based on agronomic characteristics. Testing in the Provisia Preliminary Yield (PVPY) trial in 2014 and the Provisia Multilocation Test in 2015 indicated good yield potential and favorable agronomic characteristics. In 2016 and 2017, PVL01 was evaluated in 14 replicated trials across seven locations in Louisiana. Four high-yielding commercial cultivars were included as checks, 'CL111', 'Cheniere', 'Cocodrie', and 'Mermentau'. Grain yield of PVL01 was 7.5 t ha −1 compared with 7.6 t ha −1 for CL111, 8.3 t ha −1 for Cheniere, 6.8 t ha −1 for Cocodrie, and 7.5 t ha −1 for Mermentau. PVL01 is very susceptible to blast, susceptible to sheath blight and bacterial panicle blight, and moderately resistant to Cercospora spp.
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