Rice is one of the major staple foods in the world, especially in the developing countries of Asi... more Rice is one of the major staple foods in the world, especially in the developing countries of Asia. Its consumption as a dietary source is also increasing in Africa. To meet the demand for rice to feed the increasing human population, increasing rice yield is essential. Improving the genetic yield potential of rice is one ideal solution. It is imperative to introduce the identified yield-enhancing gene(s) into modern rice cultivars for the rapid improvement of yield potential through marker-assisted breeding. We report the development of PCR-gel-based markers for eight yield-related functional genes (Gn1a, OsSPL14, SCM2, Ghd7, DEP1, SPIKE, GS5, and TGW6) to introduce yield-positive alleles from the donor lines. Six rice cultivars, including three each of donor and recipient lines, respectively, were sequenced by next-generation whole-genome sequencing to detect DNA polymorphisms between the genotypes. Additionally, PCR products containing functional nucleotide polymorphism (FNP) or ...
The genus Oryza, which includes the Asian (O. sativa) and African (O. glaberrima) cultivated rice... more The genus Oryza, which includes the Asian (O. sativa) and African (O. glaberrima) cultivated rices and all of their 21 wild relatives, represents 15 million years of evolution. We compared the regulation of putative orthologous groups of stress related transcription factors (TFs) as an initial effort to address the question of functional conservation, and to dissect a continuum of stress response genetic network complexities that might have emerged during the closely spaced Oryza speciation and domestication events. Eight groups of putative orthologous TFs, including six DREB/CBF, one Myb4, and one bZIP-TGA10 were compared among cultivated and wild species representing most of the known diploid genomes (AA, BB, CC, EE, FF), in terms of expression patterns across a battery of stress regimes (cold, heat, salinity, rapid dehydration) and regulatory information content of upstream regions of each gene. Two important trends had emerged from these studies. First, for most of the genes, ex...
Biotic stresses such as bacterial leaf blight (BB), Blast and brown planthopper (BPH) are major t... more Biotic stresses such as bacterial leaf blight (BB), Blast and brown planthopper (BPH) are major threats to rice production in South and Southeast Asia. Several single genes conferring resistance to these diseases and insect resistance have lost their resistance due to changes in insect biotypes and disease races in recent years. Thus, there is a need to breed for rice varieties with durable and broad spectrum of resistance to insect pests and diseases. In this study, we transferred three resistance (R) genes, Xa4, xa5 and Xa21 for BB, one (Pi40) for blast and one (Bph18) for BPH from one japonica breeding line, IR 90751-1-14-1-2 into two elite indica varieties (IR72 and NSIC Rc222) genetic background by backcross breeding and marker assisted selection (MAS) using gene-specific, STS and CAPS markers. Initially, F1 plants with confirmed multiple R genes in heterozygous state were backcrossed with the respective recurrent parents and a set of segregating backcross progenies were develo...
The genomic structure of Oryza species is informative to widen the genetic base and to design str... more The genomic structure of Oryza species is informative to widen the genetic base and to design strategies for more efficient rice improvement programs. 384-plex GoldenGate SNP genotyping of 48 accessions of cultivated and wild species were used to determine the population structure and to explore the variation in stigma and style length of Oryza species. More than 98 % of the SNPs were amplified in O. sativa subspecies indica and japonica whereas, among the AA genome wild species, O. longistaminata and O. meridionalis had the lowest amplification of 80 and 72 %, respectively. Population structure analysis grouped the 48 accessions into six subpopulations: I. O. sativa subspecies indica, II. O. sativa subspecies japonica, III. O. nivara, IV. O. sativa complex, V. O. officinalis complex, and VI. O. meyeriana and O. ridleyi complex. Phylogentic analysis based on evolutionary dissimilarities supported most of the groupings done in the bayesian cluster analysis. A wide range of variability was present for pistil characteristics in Oryza species. Among the wild species in the AA genome, O. longistaminata has significantly longer stigma, style, and total pistil length than the remaining Oryza species. We identified five SNP loci on chromosomes 3, 4, 7, and 10 that have shown significant association with stigma length, style length, and stigma plus style length, and explained 17–24 % of the phenotypic variation. The present study is useful to unravel the mechanisms governing natural genetic variation for stigma length which will be useful in improving out-crossing rate in rice for increased hybrid seed production.
Rice is one of the major staple foods in the world, especially in the developing countries of Asi... more Rice is one of the major staple foods in the world, especially in the developing countries of Asia. Its consumption as a dietary source is also increasing in Africa. To meet the demand for rice to feed the increasing human population, increasing rice yield is essential. Improving the genetic yield potential of rice is one ideal solution. It is imperative to introduce the identified yield-enhancing gene(s) into modern rice cultivars for the rapid improvement of yield potential through marker-assisted breeding. We report the development of PCR-gel-based markers for eight yield-related functional genes (Gn1a, OsSPL14, SCM2, Ghd7, DEP1, SPIKE, GS5, and TGW6) to introduce yield-positive alleles from the donor lines. Six rice cultivars, including three each of donor and recipient lines, respectively, were sequenced by next-generation whole-genome sequencing to detect DNA polymorphisms between the genotypes. Additionally, PCR products containing functional nucleotide polymorphism (FNP) or ...
The genus Oryza, which includes the Asian (O. sativa) and African (O. glaberrima) cultivated rice... more The genus Oryza, which includes the Asian (O. sativa) and African (O. glaberrima) cultivated rices and all of their 21 wild relatives, represents 15 million years of evolution. We compared the regulation of putative orthologous groups of stress related transcription factors (TFs) as an initial effort to address the question of functional conservation, and to dissect a continuum of stress response genetic network complexities that might have emerged during the closely spaced Oryza speciation and domestication events. Eight groups of putative orthologous TFs, including six DREB/CBF, one Myb4, and one bZIP-TGA10 were compared among cultivated and wild species representing most of the known diploid genomes (AA, BB, CC, EE, FF), in terms of expression patterns across a battery of stress regimes (cold, heat, salinity, rapid dehydration) and regulatory information content of upstream regions of each gene. Two important trends had emerged from these studies. First, for most of the genes, ex...
Biotic stresses such as bacterial leaf blight (BB), Blast and brown planthopper (BPH) are major t... more Biotic stresses such as bacterial leaf blight (BB), Blast and brown planthopper (BPH) are major threats to rice production in South and Southeast Asia. Several single genes conferring resistance to these diseases and insect resistance have lost their resistance due to changes in insect biotypes and disease races in recent years. Thus, there is a need to breed for rice varieties with durable and broad spectrum of resistance to insect pests and diseases. In this study, we transferred three resistance (R) genes, Xa4, xa5 and Xa21 for BB, one (Pi40) for blast and one (Bph18) for BPH from one japonica breeding line, IR 90751-1-14-1-2 into two elite indica varieties (IR72 and NSIC Rc222) genetic background by backcross breeding and marker assisted selection (MAS) using gene-specific, STS and CAPS markers. Initially, F1 plants with confirmed multiple R genes in heterozygous state were backcrossed with the respective recurrent parents and a set of segregating backcross progenies were develo...
The genomic structure of Oryza species is informative to widen the genetic base and to design str... more The genomic structure of Oryza species is informative to widen the genetic base and to design strategies for more efficient rice improvement programs. 384-plex GoldenGate SNP genotyping of 48 accessions of cultivated and wild species were used to determine the population structure and to explore the variation in stigma and style length of Oryza species. More than 98 % of the SNPs were amplified in O. sativa subspecies indica and japonica whereas, among the AA genome wild species, O. longistaminata and O. meridionalis had the lowest amplification of 80 and 72 %, respectively. Population structure analysis grouped the 48 accessions into six subpopulations: I. O. sativa subspecies indica, II. O. sativa subspecies japonica, III. O. nivara, IV. O. sativa complex, V. O. officinalis complex, and VI. O. meyeriana and O. ridleyi complex. Phylogentic analysis based on evolutionary dissimilarities supported most of the groupings done in the bayesian cluster analysis. A wide range of variability was present for pistil characteristics in Oryza species. Among the wild species in the AA genome, O. longistaminata has significantly longer stigma, style, and total pistil length than the remaining Oryza species. We identified five SNP loci on chromosomes 3, 4, 7, and 10 that have shown significant association with stigma length, style length, and stigma plus style length, and explained 17–24 % of the phenotypic variation. The present study is useful to unravel the mechanisms governing natural genetic variation for stigma length which will be useful in improving out-crossing rate in rice for increased hybrid seed production.
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Papers by Sherry Hechanova
accessions of cultivated and wild species were used to determine the population structure and to explore the variation in stigma and style length of Oryza species. More than 98 % of the SNPs were amplified in O. sativa subspecies indica and japonica whereas, among the AA genome wild species, O. longistaminata and O. meridionalis had the lowest amplification of 80 and 72 %, respectively. Population structure analysis grouped the 48 accessions into six subpopulations: I. O. sativa subspecies indica, II. O. sativa subspecies japonica, III. O. nivara, IV. O. sativa complex, V. O. officinalis complex, and VI. O. meyeriana and O.
ridleyi complex. Phylogentic analysis based on evolutionary dissimilarities supported most of the groupings done in the bayesian cluster analysis. A wide range of variability was present for pistil characteristics in Oryza species. Among the wild species in the AA genome, O. longistaminata has significantly longer stigma, style, and total pistil length than the remaining Oryza species. We identified five SNP loci on chromosomes 3, 4, 7, and 10 that have shown significant association with stigma length, style length, and stigma plus style length, and explained 17–24 % of the phenotypic variation. The present study is useful to unravel the mechanisms governing natural genetic variation for stigma length which will be useful in improving out-crossing rate in rice for increased hybrid seed production.
accessions of cultivated and wild species were used to determine the population structure and to explore the variation in stigma and style length of Oryza species. More than 98 % of the SNPs were amplified in O. sativa subspecies indica and japonica whereas, among the AA genome wild species, O. longistaminata and O. meridionalis had the lowest amplification of 80 and 72 %, respectively. Population structure analysis grouped the 48 accessions into six subpopulations: I. O. sativa subspecies indica, II. O. sativa subspecies japonica, III. O. nivara, IV. O. sativa complex, V. O. officinalis complex, and VI. O. meyeriana and O.
ridleyi complex. Phylogentic analysis based on evolutionary dissimilarities supported most of the groupings done in the bayesian cluster analysis. A wide range of variability was present for pistil characteristics in Oryza species. Among the wild species in the AA genome, O. longistaminata has significantly longer stigma, style, and total pistil length than the remaining Oryza species. We identified five SNP loci on chromosomes 3, 4, 7, and 10 that have shown significant association with stigma length, style length, and stigma plus style length, and explained 17–24 % of the phenotypic variation. The present study is useful to unravel the mechanisms governing natural genetic variation for stigma length which will be useful in improving out-crossing rate in rice for increased hybrid seed production.