There is a large gap between genomewide association studies (GWAS) and developing markers that ca... more There is a large gap between genomewide association studies (GWAS) and developing markers that can be used in marker‐assisted selection (MAS) schemes for cultivar improvement. This study is a prototype for developing markers using segregating single nucleotide polymorphisms (SNPs) for panicle architecture and grain shape traits identified by GWAS in the Rice Diversity Panel‐1 and colocalized in QTL regions revealed by linkage mapping in the Estrela × NSFTV199 rice (Oryza sativa L.) population. Markers were developed from sequence variants suitable for reliable detection in regions surrounding the most significant SNPs identified in GWAS. Once developed, the markers were validated in three Japonica subspecies biparental populations, used to improve QTL mapping resolution, and employed to select potential parents for use in MAS. All marker alleles segregated in the rice tropical japonica subpopulation.
Crop wild relatives represent valuable reservoirs of variation for breeding, but their population... more Crop wild relatives represent valuable reservoirs of variation for breeding, but their populations are threatened in natural habitats, are sparsely represented in genebanks, and most are poorly characterized. The focus of this study is the Oryza rufipogon species complex (ORSC), wild progenitor of Asian rice (Oryza sativa L.). The ORSC comprises perennial, annual and intermediate forms which were historically designated as O. rufipogon, O. nivara, and O. sativa f. spontanea (or Oryza spp., an annual form of mixed O. rufipogon/O. nivara and O. sativa ancestry), respectively, based on non-standardized morphological, geographical, and/or ecologically-based species definitions and boundaries. Here, a collection of 240 diverse ORSC accessions, characterized by genotyping-by-sequencing (113,739 SNPs), was phenotyped for 44 traits associated with plant, panicle, and seed morphology in the screenhouse at the International Rice Research Institute, Philippines. These traits included heritable...
Amphiploids of tall fescue (Festuca arundinacea Schreb.) and giant fescue [F. gigantea (L.) Vill.... more Amphiploids of tall fescue (Festuca arundinacea Schreb.) and giant fescue [F. gigantea (L.) Vill.] have high forage quality but are meiotically irregular and have low seed yield. The objective of this study was to evaluate effects of generation advance and cytoplasm on meiotic behavior of tall fescue ✕ giant fescue amphiploid derivatives. Chromosome number and pairing, frequency of micronuclei, and pollen stainability were analyzed in 75 amphiploids developed from reciprocal hybrids of giant fescue ✕ tall fescue (including derivatives of annual ryegrass [Lolium multiflorum Lam.] ✕ tall fescue). Amphiploids represented five generations (C1–C5) of maternal half‐sib progenies in three cytoplasmic backgrounds (annual ryegrass, giant fescue, and tall fescue). Chromosomes were lost and meiotic irregularity increased over generations. Chromosome number at C1 averaged 2n = 83.5 (range 2n = 81 to 84) and at C5 averaged 2n = 74.9 (range 2n = 48 to 84). The frequencies univalents and trivalent...
Asian rice (Oryza sativa L.) is divided into two major subspecies, Indica and Japonica with the t... more Asian rice (Oryza sativa L.) is divided into two major subspecies, Indica and Japonica with the temperate and tropical japonica subpopulations being part of Japonica. These two subpopulations encompass the majority of the rice grown in the USA. Recently, a genome-wide association study (GWAS) identified SNP markers associated with 32 traits of agronomic importance. To validate these associations, four bi-parental recombinant inbred line (RIL) populations are currently under development using Japonica parents that were extreme for several of the traits evaluated. Two populations (Estrela x NSFTV 199; Norin 20 x Fortuna) were evaluated in the field during summer 2012 in an unreplicated study to observe the phenotypic variation and produce enough seed for replicated field studies. Transgressive variation was observed for days to heading, plant height and plant type (tiller angle). Data on panicle and seed traits (panicle length, primary panicle branch number, seeds per panicle, seed si...
This study was conducted using the isozymes ACP-1, ADH-1, GOT-2, GOT-3, MDH, 6-PGD-1 and PGI-2 to... more This study was conducted using the isozymes ACP-1, ADH-1, GOT-2, GOT-3, MDH, 6-PGD-1 and PGI-2 to: a) compare isozyme banding patterns of tall fescue somaclones with parents and b) correlate tissue culture-induced chromosome abnormalities with variant banding patterns. The 174 somaclones were grouped into seven categories based on their meiotic analyses and time of regeneration from culture. Differences in isozyme
There is a large gap between genomewide association studies (GWAS) and developing markers that ca... more There is a large gap between genomewide association studies (GWAS) and developing markers that can be used in marker‐assisted selection (MAS) schemes for cultivar improvement. This study is a prototype for developing markers using segregating single nucleotide polymorphisms (SNPs) for panicle architecture and grain shape traits identified by GWAS in the Rice Diversity Panel‐1 and colocalized in QTL regions revealed by linkage mapping in the Estrela × NSFTV199 rice (Oryza sativa L.) population. Markers were developed from sequence variants suitable for reliable detection in regions surrounding the most significant SNPs identified in GWAS. Once developed, the markers were validated in three Japonica subspecies biparental populations, used to improve QTL mapping resolution, and employed to select potential parents for use in MAS. All marker alleles segregated in the rice tropical japonica subpopulation.
Crop wild relatives represent valuable reservoirs of variation for breeding, but their population... more Crop wild relatives represent valuable reservoirs of variation for breeding, but their populations are threatened in natural habitats, are sparsely represented in genebanks, and most are poorly characterized. The focus of this study is the Oryza rufipogon species complex (ORSC), wild progenitor of Asian rice (Oryza sativa L.). The ORSC comprises perennial, annual and intermediate forms which were historically designated as O. rufipogon, O. nivara, and O. sativa f. spontanea (or Oryza spp., an annual form of mixed O. rufipogon/O. nivara and O. sativa ancestry), respectively, based on non-standardized morphological, geographical, and/or ecologically-based species definitions and boundaries. Here, a collection of 240 diverse ORSC accessions, characterized by genotyping-by-sequencing (113,739 SNPs), was phenotyped for 44 traits associated with plant, panicle, and seed morphology in the screenhouse at the International Rice Research Institute, Philippines. These traits included heritable...
Amphiploids of tall fescue (Festuca arundinacea Schreb.) and giant fescue [F. gigantea (L.) Vill.... more Amphiploids of tall fescue (Festuca arundinacea Schreb.) and giant fescue [F. gigantea (L.) Vill.] have high forage quality but are meiotically irregular and have low seed yield. The objective of this study was to evaluate effects of generation advance and cytoplasm on meiotic behavior of tall fescue ✕ giant fescue amphiploid derivatives. Chromosome number and pairing, frequency of micronuclei, and pollen stainability were analyzed in 75 amphiploids developed from reciprocal hybrids of giant fescue ✕ tall fescue (including derivatives of annual ryegrass [Lolium multiflorum Lam.] ✕ tall fescue). Amphiploids represented five generations (C1–C5) of maternal half‐sib progenies in three cytoplasmic backgrounds (annual ryegrass, giant fescue, and tall fescue). Chromosomes were lost and meiotic irregularity increased over generations. Chromosome number at C1 averaged 2n = 83.5 (range 2n = 81 to 84) and at C5 averaged 2n = 74.9 (range 2n = 48 to 84). The frequencies univalents and trivalent...
Asian rice (Oryza sativa L.) is divided into two major subspecies, Indica and Japonica with the t... more Asian rice (Oryza sativa L.) is divided into two major subspecies, Indica and Japonica with the temperate and tropical japonica subpopulations being part of Japonica. These two subpopulations encompass the majority of the rice grown in the USA. Recently, a genome-wide association study (GWAS) identified SNP markers associated with 32 traits of agronomic importance. To validate these associations, four bi-parental recombinant inbred line (RIL) populations are currently under development using Japonica parents that were extreme for several of the traits evaluated. Two populations (Estrela x NSFTV 199; Norin 20 x Fortuna) were evaluated in the field during summer 2012 in an unreplicated study to observe the phenotypic variation and produce enough seed for replicated field studies. Transgressive variation was observed for days to heading, plant height and plant type (tiller angle). Data on panicle and seed traits (panicle length, primary panicle branch number, seeds per panicle, seed si...
This study was conducted using the isozymes ACP-1, ADH-1, GOT-2, GOT-3, MDH, 6-PGD-1 and PGI-2 to... more This study was conducted using the isozymes ACP-1, ADH-1, GOT-2, GOT-3, MDH, 6-PGD-1 and PGI-2 to: a) compare isozyme banding patterns of tall fescue somaclones with parents and b) correlate tissue culture-induced chromosome abnormalities with variant banding patterns. The 174 somaclones were grouped into seven categories based on their meiotic analyses and time of regeneration from culture. Differences in isozyme
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