A meta-analysis of quantitative trait loci (QTL) associated with plant digestibility and cell wal... more A meta-analysis of quantitative trait loci (QTL) associated with plant digestibility and cell wall composition in maize was carried out using results from 11 different mapping experiments. Statistical methods implemented in ''MetaQTL'' software were used to build a consensus map, project QTL positions and perform meta-analysis. Fiftynine QTL for traits associated with digestibility and 150 QTL for traits associated with cell wall composition were included in the analysis. We identified 26 and 42 metaQTL for digestibility and cell wall composition traits, respectively. Fifteen metaQTL with confidence interval (CI) smaller than 10 cM were identified. As expected from trait correlations, 42% of metaQTL for digestibility displayed overlapping CIs with metaQTL for cell wall composition traits. Coincidences were particularly strong on chromosomes 1 and 3. In a second step, 356 genes selected from the MAIZEWALL database as candidates for the cell wall biosynthesis pathway were positioned on our consensus map. Colocalizations between candidate genes and meta-QTL positions appeared globally significant based on v 2 tests. This study contributed in identifying key chromosomal regions involved in silage quality and potentially associated genes for most of these regions. These genes deserve further investigation, in particular through association mapping.
Quantitative genetics, genomics and plant breeding, 2001
... Inc., PO Box 609, Waimea, HI 96796, USA Introduction The application of molecular markers to ... more ... Inc., PO Box 609, Waimea, HI 96796, USA Introduction The application of molecular markers to plant breeding can be divided ... of the target trait; and (iii) fol-lowing the identification of the genomic regions of interest, crop improvement through marker-assisted selection (MAS). ...
Abstract Drought is the single most common cause of severe crop production shortage in developing... more Abstract Drought is the single most common cause of severe crop production shortage in developing countries, and global warming is predicted to further exacerbate drought's impact. This chapter describes how to best evaluate segregating germplasm under water-limited conditions, ...
A meta-analysis of quantitative trait loci (QTL) associated with plant digestibility and cell wal... more A meta-analysis of quantitative trait loci (QTL) associated with plant digestibility and cell wall composition in maize was carried out using results from 11 different mapping experiments. Statistical methods implemented in ''MetaQTL'' software were used to build a consensus map, project QTL positions and perform meta-analysis. Fiftynine QTL for traits associated with digestibility and 150 QTL for traits associated with cell wall composition were included in the analysis. We identified 26 and 42 metaQTL for digestibility and cell wall composition traits, respectively. Fifteen metaQTL with confidence interval (CI) smaller than 10 cM were identified. As expected from trait correlations, 42% of metaQTL for digestibility displayed overlapping CIs with metaQTL for cell wall composition traits. Coincidences were particularly strong on chromosomes 1 and 3. In a second step, 356 genes selected from the MAIZEWALL database as candidates for the cell wall biosynthesis pathway were positioned on our consensus map. Colocalizations between candidate genes and meta-QTL positions appeared globally significant based on v 2 tests. This study contributed in identifying key chromosomal regions involved in silage quality and potentially associated genes for most of these regions. These genes deserve further investigation, in particular through association mapping.
Recent progress in genotyping and resequencing techniques have opened new opportunities for decip... more Recent progress in genotyping and resequencing techniques have opened new opportunities for deciphering quantitative trait variation by looking for associations between traits of interest and polymorphisms in panels of diverse inbred lines. Association mapping raises specific issues related to the choice of appropriate (i) panels and marker-densities and (ii) statistical methods to capture associations. In this study, we used a panel of 314 maize inbred lines from the dent pool, composed of inbred material from public institutes (113 inbred lines) and a private company (201 inbred lines). We showed that local LD was higher and genetic diversity lower in the material of private origin than in the public material. We compared the results obtained by different software for identifying population structure and computing relatedness among lines, and ran association tests for earliness related traits. Our results confirmed the importance of the mite polymorphism of Vgt1 on flowering time, but also showed that its effect can be captured by zmRap2.7 polymorphisms located 70 kb apart. We also highlighted associations with polymorphisms within genes putatively involved in lignin biosynthesis pathway, which deserve further investigations.
A meta-analysis of quantitative trait loci (QTL) associated with plant digestibility and cell wal... more A meta-analysis of quantitative trait loci (QTL) associated with plant digestibility and cell wall composition in maize was carried out using results from 11 different mapping experiments. Statistical methods implemented in ''MetaQTL'' software were used to build a consensus map, project QTL positions and perform meta-analysis. Fiftynine QTL for traits associated with digestibility and 150 QTL for traits associated with cell wall composition were included in the analysis. We identified 26 and 42 metaQTL for digestibility and cell wall composition traits, respectively. Fifteen metaQTL with confidence interval (CI) smaller than 10 cM were identified. As expected from trait correlations, 42% of metaQTL for digestibility displayed overlapping CIs with metaQTL for cell wall composition traits. Coincidences were particularly strong on chromosomes 1 and 3. In a second step, 356 genes selected from the MAIZEWALL database as candidates for the cell wall biosynthesis pathway were positioned on our consensus map. Colocalizations between candidate genes and meta-QTL positions appeared globally significant based on v 2 tests. This study contributed in identifying key chromosomal regions involved in silage quality and potentially associated genes for most of these regions. These genes deserve further investigation, in particular through association mapping.
Quantitative genetics, genomics and plant breeding, 2001
... Inc., PO Box 609, Waimea, HI 96796, USA Introduction The application of molecular markers to ... more ... Inc., PO Box 609, Waimea, HI 96796, USA Introduction The application of molecular markers to plant breeding can be divided ... of the target trait; and (iii) fol-lowing the identification of the genomic regions of interest, crop improvement through marker-assisted selection (MAS). ...
Abstract Drought is the single most common cause of severe crop production shortage in developing... more Abstract Drought is the single most common cause of severe crop production shortage in developing countries, and global warming is predicted to further exacerbate drought's impact. This chapter describes how to best evaluate segregating germplasm under water-limited conditions, ...
A meta-analysis of quantitative trait loci (QTL) associated with plant digestibility and cell wal... more A meta-analysis of quantitative trait loci (QTL) associated with plant digestibility and cell wall composition in maize was carried out using results from 11 different mapping experiments. Statistical methods implemented in ''MetaQTL'' software were used to build a consensus map, project QTL positions and perform meta-analysis. Fiftynine QTL for traits associated with digestibility and 150 QTL for traits associated with cell wall composition were included in the analysis. We identified 26 and 42 metaQTL for digestibility and cell wall composition traits, respectively. Fifteen metaQTL with confidence interval (CI) smaller than 10 cM were identified. As expected from trait correlations, 42% of metaQTL for digestibility displayed overlapping CIs with metaQTL for cell wall composition traits. Coincidences were particularly strong on chromosomes 1 and 3. In a second step, 356 genes selected from the MAIZEWALL database as candidates for the cell wall biosynthesis pathway were positioned on our consensus map. Colocalizations between candidate genes and meta-QTL positions appeared globally significant based on v 2 tests. This study contributed in identifying key chromosomal regions involved in silage quality and potentially associated genes for most of these regions. These genes deserve further investigation, in particular through association mapping.
Recent progress in genotyping and resequencing techniques have opened new opportunities for decip... more Recent progress in genotyping and resequencing techniques have opened new opportunities for deciphering quantitative trait variation by looking for associations between traits of interest and polymorphisms in panels of diverse inbred lines. Association mapping raises specific issues related to the choice of appropriate (i) panels and marker-densities and (ii) statistical methods to capture associations. In this study, we used a panel of 314 maize inbred lines from the dent pool, composed of inbred material from public institutes (113 inbred lines) and a private company (201 inbred lines). We showed that local LD was higher and genetic diversity lower in the material of private origin than in the public material. We compared the results obtained by different software for identifying population structure and computing relatedness among lines, and ran association tests for earliness related traits. Our results confirmed the importance of the mite polymorphism of Vgt1 on flowering time, but also showed that its effect can be captured by zmRap2.7 polymorphisms located 70 kb apart. We also highlighted associations with polymorphisms within genes putatively involved in lignin biosynthesis pathway, which deserve further investigations.
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Papers by J. Betran