Page 1. Genetic Analysis of Drought Resistance in Rice by Molecular Markers: Association between ... more Page 1. Genetic Analysis of Drought Resistance in Rice by Molecular Markers: Association between Secondary Traits and Field Performance R. Chandra Babu,* Bay D. Nguyen, Varapong Chamarerk, P. Shanmugasundaram ...
Page 1. Genetic Analysis of Drought Resistance in Rice by Molecular Markers: Association between ... more Page 1. Genetic Analysis of Drought Resistance in Rice by Molecular Markers: Association between Secondary Traits and Field Performance R. Chandra Babu,* Bay D. Nguyen, Varapong Chamarerk, P. Shanmugasundaram ...
Direct and indirect economic loss in the agricultural sector due to drought is huge. With the adv... more Direct and indirect economic loss in the agricultural sector due to drought is huge. With the advent of molecular-marker technology, research on drought resistance in crop plants has shifted from physiological descriptions of the phenomenon to genetic dissection of the mechanisms involved. Here, we report a comprehensive study of mapping the drought resistance components (osmotic adjustment and root traits) in a doubled-haploid rice (Oryza sativa L.) population of 154 lines. A genetic linkage map consisting of 315 DNA markers was constructed. A total of 41 quantitative trait loci (QTLs) were identified for osmotic adjustment and root traits, and individually explained 8–38% of the phenotypic variance. A region on chromosome 4 harbored major QTLs for several root traits. Consistent QTLs for drought responses across genetic backgrounds were detected and should be useful for marker-assisted selection towards the incorporation of a trait of interest into an elite line. Comparative mapping identified three conserved genomic regions associated with various physiological responses to drought in several grass species. These results suggest that these regions conferring drought adaptation have been conserved across grass species during genome evolution and might be directly applied across species for the improvement of drought resistance in cereal crops.
Understanding the series of events that causes a symptomatic disease response brings to light the... more Understanding the series of events that causes a symptomatic disease response brings to light the relationship between a pathogen and its host. More than 50 bacteria, fungi, virus, and nematodes have been implicated in cotton diseases that annually account for an estimated $897 million in lost revenue to the U.S. crop. Advances in cotton genetics have led to the development of several technologies that enable the detailed examination of the cotton genome for genes that function in response to pathogen infection. There is an opportunity to make direct and meaningful comparisons from data generated by forward and reverse genetics. Comparing QTL information with reverse genetics (functional genomics) offers a powerful approach to identify and characterize the key pathways and the genetics involved in disease. Cotton is an interesting taxon in which to study disease because its evolution includes the divergence of resistance (R-genes) through the radiation of species, as well as multiple genetic bottlenecks including polyploid formation and the domestication of a small subset of Gossypium species.
Black root rot (BRR), incited by the soilborne pathogen Thielaviopsis basicola has the potential ... more Black root rot (BRR), incited by the soilborne pathogen Thielaviopsis basicola has the potential to cause significant economic loss in cotton (Gossypium spp.) production. Cultivated tetraploids of cotton (G. hirsutum and G. barbadense) are susceptible although resistant types have been identified in a possible tetraploid progenitor, G. herbaceum. Genetic mapping was used to detect the chromosomal locations of quantitative trait loci (QTL) that confer resistance to the BRR pathogen. A population of F2 individuals (G. herbaceum × G. arboreum) and F2:3 progeny families were examined. Phenotypic variation between resistant and susceptible reactions could be explained partly by three QTL. The BRR5.1, BRR9.1, and BRR13.1 QTL each explained 19.1, 10.3 and 8.5% of the total phenotypic variation, respectively. The combination of all three in a single genetic model explained 32.7% of the phenotypic variation. Comparative analysis was conducted on significant QTL regions to deduce the cotton–Arabidopsis synteny relationship and examine the correspondence between BRR QTL and Arabidopsis pathogen defense genes. Totally 20 Arabidopsis synteny segments corresponded within one of three BRR QTL regions. Each synteny segment contains many potential Arabidopsis candidate genes. A total of 624 Arabidopsis genes, including 22 pathogen defense and 36 stress response genes, could be placed within the syntenic regions corresponding to the BRR QTL. Fine mapping is needed to delineate each underlying BRR R-gene and possible Arabidopsis orthologs. Research and breeding activities to examine each QTL and underlying genes in Upland cotton (G. hirsutum) are ongoing.
Development of gene therapies for wound healing will depend on the identification of the genes in... more Development of gene therapies for wound healing will depend on the identification of the genes involved in wound healing and tissue regeneration. Previous quantitative trait loci (QTL) studies in mice using the ear punch model have shown that major QTL exist on chromosome (Chr) 9 for soft tissue regeneration. In this study, we have developed a congenic line that contains the Chr 9 QTL chromosomal region from super healer MRL/MpJ in the genomic background of poor-healing SJL/J. The phenotypic effect of this QTL was confirmed in male mice, where the congenic line has shown significant healing improvement over SJL. Fine mapping of the Chr 9 QTL region with 23 markers at an average distance of 4.2 Mb using a total of 1,564 MRL/MpJ × SJL/J F2 mice revealed the presence of at least three QTL peaks, implying that three separate loci may contribute to the phenotypic effect of this QTL. Based on the 2-LOD intervals, the total QTL region was confined to a combined length of no more than 28.2 Mb. Application of a Bayesian shrinkage estimation indicated that a major locus was located in a region of just 1.3 Mb.
Wound healing/regeneration mouse models are few, and studies performed have mainly utilized cross... more Wound healing/regeneration mouse models are few, and studies performed have mainly utilized crosses between MRL/MPJ (a good healer) and SJL/J (a poor healer) or MRL/lpr (a good healer) and C57BL/6J (a poor healer). Wound healing is a complex trait with many genes involved in the expression of the phenotype. Based on data from previous studies that common and additional quantitative trait loci (QTL) were identified using different crosses of inbred strains of mice for various complex traits, we hypothesized that a new cross would identify common and additional QTL, unique modes of inheritance, and interacting loci, which are responsible for variation in susceptibility to fast wound healing. In this study, we crossed DBA/1J (DBA, a good healer) and 129/SvJ (129, a poor healer) and performed a genome-wide scan using 492 (DBA×129) F2 mice and 98 markers to identify QTL that regulate wound healing/regeneration. Four QTL on chromosomes 1, 4, 12, and 18 were identified which contributed toward wound healing in F2 mice and accounted for 17.1% of the phenotypic variation in ear punch healing. Surprisingly, locus interactions contributed to 55.7% of the phenotype variation in ear punch healing. In conclusion, we have identified novel QTL and shown that minor interacting loci contribute significantly to wound healing in DBA×129 mice cross.
Page 1. Genetic Analysis of Drought Resistance in Rice by Molecular Markers: Association between ... more Page 1. Genetic Analysis of Drought Resistance in Rice by Molecular Markers: Association between Secondary Traits and Field Performance R. Chandra Babu,* Bay D. Nguyen, Varapong Chamarerk, P. Shanmugasundaram ...
Page 1. Genetic Analysis of Drought Resistance in Rice by Molecular Markers: Association between ... more Page 1. Genetic Analysis of Drought Resistance in Rice by Molecular Markers: Association between Secondary Traits and Field Performance R. Chandra Babu,* Bay D. Nguyen, Varapong Chamarerk, P. Shanmugasundaram ...
Direct and indirect economic loss in the agricultural sector due to drought is huge. With the adv... more Direct and indirect economic loss in the agricultural sector due to drought is huge. With the advent of molecular-marker technology, research on drought resistance in crop plants has shifted from physiological descriptions of the phenomenon to genetic dissection of the mechanisms involved. Here, we report a comprehensive study of mapping the drought resistance components (osmotic adjustment and root traits) in a doubled-haploid rice (Oryza sativa L.) population of 154 lines. A genetic linkage map consisting of 315 DNA markers was constructed. A total of 41 quantitative trait loci (QTLs) were identified for osmotic adjustment and root traits, and individually explained 8–38% of the phenotypic variance. A region on chromosome 4 harbored major QTLs for several root traits. Consistent QTLs for drought responses across genetic backgrounds were detected and should be useful for marker-assisted selection towards the incorporation of a trait of interest into an elite line. Comparative mapping identified three conserved genomic regions associated with various physiological responses to drought in several grass species. These results suggest that these regions conferring drought adaptation have been conserved across grass species during genome evolution and might be directly applied across species for the improvement of drought resistance in cereal crops.
Understanding the series of events that causes a symptomatic disease response brings to light the... more Understanding the series of events that causes a symptomatic disease response brings to light the relationship between a pathogen and its host. More than 50 bacteria, fungi, virus, and nematodes have been implicated in cotton diseases that annually account for an estimated $897 million in lost revenue to the U.S. crop. Advances in cotton genetics have led to the development of several technologies that enable the detailed examination of the cotton genome for genes that function in response to pathogen infection. There is an opportunity to make direct and meaningful comparisons from data generated by forward and reverse genetics. Comparing QTL information with reverse genetics (functional genomics) offers a powerful approach to identify and characterize the key pathways and the genetics involved in disease. Cotton is an interesting taxon in which to study disease because its evolution includes the divergence of resistance (R-genes) through the radiation of species, as well as multiple genetic bottlenecks including polyploid formation and the domestication of a small subset of Gossypium species.
Black root rot (BRR), incited by the soilborne pathogen Thielaviopsis basicola has the potential ... more Black root rot (BRR), incited by the soilborne pathogen Thielaviopsis basicola has the potential to cause significant economic loss in cotton (Gossypium spp.) production. Cultivated tetraploids of cotton (G. hirsutum and G. barbadense) are susceptible although resistant types have been identified in a possible tetraploid progenitor, G. herbaceum. Genetic mapping was used to detect the chromosomal locations of quantitative trait loci (QTL) that confer resistance to the BRR pathogen. A population of F2 individuals (G. herbaceum × G. arboreum) and F2:3 progeny families were examined. Phenotypic variation between resistant and susceptible reactions could be explained partly by three QTL. The BRR5.1, BRR9.1, and BRR13.1 QTL each explained 19.1, 10.3 and 8.5% of the total phenotypic variation, respectively. The combination of all three in a single genetic model explained 32.7% of the phenotypic variation. Comparative analysis was conducted on significant QTL regions to deduce the cotton–Arabidopsis synteny relationship and examine the correspondence between BRR QTL and Arabidopsis pathogen defense genes. Totally 20 Arabidopsis synteny segments corresponded within one of three BRR QTL regions. Each synteny segment contains many potential Arabidopsis candidate genes. A total of 624 Arabidopsis genes, including 22 pathogen defense and 36 stress response genes, could be placed within the syntenic regions corresponding to the BRR QTL. Fine mapping is needed to delineate each underlying BRR R-gene and possible Arabidopsis orthologs. Research and breeding activities to examine each QTL and underlying genes in Upland cotton (G. hirsutum) are ongoing.
Development of gene therapies for wound healing will depend on the identification of the genes in... more Development of gene therapies for wound healing will depend on the identification of the genes involved in wound healing and tissue regeneration. Previous quantitative trait loci (QTL) studies in mice using the ear punch model have shown that major QTL exist on chromosome (Chr) 9 for soft tissue regeneration. In this study, we have developed a congenic line that contains the Chr 9 QTL chromosomal region from super healer MRL/MpJ in the genomic background of poor-healing SJL/J. The phenotypic effect of this QTL was confirmed in male mice, where the congenic line has shown significant healing improvement over SJL. Fine mapping of the Chr 9 QTL region with 23 markers at an average distance of 4.2 Mb using a total of 1,564 MRL/MpJ × SJL/J F2 mice revealed the presence of at least three QTL peaks, implying that three separate loci may contribute to the phenotypic effect of this QTL. Based on the 2-LOD intervals, the total QTL region was confined to a combined length of no more than 28.2 Mb. Application of a Bayesian shrinkage estimation indicated that a major locus was located in a region of just 1.3 Mb.
Wound healing/regeneration mouse models are few, and studies performed have mainly utilized cross... more Wound healing/regeneration mouse models are few, and studies performed have mainly utilized crosses between MRL/MPJ (a good healer) and SJL/J (a poor healer) or MRL/lpr (a good healer) and C57BL/6J (a poor healer). Wound healing is a complex trait with many genes involved in the expression of the phenotype. Based on data from previous studies that common and additional quantitative trait loci (QTL) were identified using different crosses of inbred strains of mice for various complex traits, we hypothesized that a new cross would identify common and additional QTL, unique modes of inheritance, and interacting loci, which are responsible for variation in susceptibility to fast wound healing. In this study, we crossed DBA/1J (DBA, a good healer) and 129/SvJ (129, a poor healer) and performed a genome-wide scan using 492 (DBA×129) F2 mice and 98 markers to identify QTL that regulate wound healing/regeneration. Four QTL on chromosomes 1, 4, 12, and 18 were identified which contributed toward wound healing in F2 mice and accounted for 17.1% of the phenotypic variation in ear punch healing. Surprisingly, locus interactions contributed to 55.7% of the phenotype variation in ear punch healing. In conclusion, we have identified novel QTL and shown that minor interacting loci contribute significantly to wound healing in DBA×129 mice cross.
Uploads
Papers by bay nguyen