Quantitative trait loci(QTL)mapping approaches rely on the correct ordering of molecular markers along the chromosomes,which can be obtained from genetic linkage maps or a reference genome sequence.For apple(Malus dom...Quantitative trait loci(QTL)mapping approaches rely on the correct ordering of molecular markers along the chromosomes,which can be obtained from genetic linkage maps or a reference genome sequence.For apple(Malus domestica Borkh),the genome sequence v1 and v2 could not meet this need;therefore,a novel approach was devised to develop a dense genetic linkage map,providing the most reliable marker-loci order for the highest possible number of markers.The approach was based on four strategies:(i)the use of multiple full-sib families,(ii)the reduction of missing information through the use of HaploBlocks and alternative calling procedures for single-nucleotide polymorphism(SNP)markers,(iii)the construction of a single backcross-type data set including all families,and(iv)a two-step map generation procedure based on the sequential inclusion of markers.The map comprises 15417 SNP markers,clustered in 3 K HaploBlock markers spanning 1267 cM,with an average distance between adjacent markers of 0.37 cM and a maximum distance of 3.29 cM.Moreover,chromosome 5 was oriented according to its homoeologous chromosome 10.This map was useful to improve the apple genome sequence,design the Axiom Apple 480 K SNP array and perform multifamily-based QTL studies.Its collinearity with the genome sequences v1 and v3 are reported.To our knowledge,this is the shortest published SNP map in apple,while including the largest number of markers,families and individuals.This result validates our methodology,proving its value for the construction of integrated linkage maps for any outbreeding species.展开更多
Plant responses to drought are regulated by complex genetic and epigenetic networks leading to rapid reprogramming of plant growth, miRNAs have been widely indicated as key players in the regulation of growth and deve...Plant responses to drought are regulated by complex genetic and epigenetic networks leading to rapid reprogramming of plant growth, miRNAs have been widely indicated as key players in the regulation of growth and development. The role of miRNAs in drought response was investigated in young leaves of Brachypodium dis- tachyon, a drought-tolerant monocot model species. Adopting an in vivo drought assay, shown to cause a dramatic reduction in leaf size, mostly due to reduced cell expansion, small RNA libraries were produced from proliferating and expanding leaf cells. Next-generation sequencing data were analyzed using an in-house bioinformatics pipeline allowing the identification of 66 annotated miRNA genes and 122 new high confidence predictions greatly expand- ing the number of known Brachypodium miRNAs. In addition, we identified four TAS3 loci and a large number of siRNA-producing loci that show characteristics suggesting that they may represent young miRNA genes. Most miR- NAs showed a high expression level, consistent with their involvement in early leaf development and cell identity. Proliferating and expanding leaf cells respond differently to drought treatment and differential expression analyses suggest novel evidence for an miRNA regulatory network controlling cell division in both normal and stressed condi-tions and demonstrate that drought trigger a genetic reprogramming of leaf growth in which miRNAs are deeply involved.展开更多
The timing of major life-history events, such as migration and moult, is set by endogenous circa-dian and circannual clocks, that have been well characterized at the molecular level. Conversely,the genetic sources of ...The timing of major life-history events, such as migration and moult, is set by endogenous circa-dian and circannual clocks, that have been well characterized at the molecular level. Conversely,the genetic sources of variation in phenology and in other behavioral traits have been sparsely ad-dressed. It has been proposed that inter-individual variability in the timing of seasonal events mayarise from allelic polymorphism at phenological candidate genes involved in the signaling cascadeof the endogenous clocks. In this study of a long-distance migratory passerine bird, the willowwarbler Phylloscopus trochilus, we investigated whether allelic variation at 5 polymorphic loci of 4candidate genes （Adcyapl, Clock, Crebl, and Npas2）, predicted 2 major components of the annualschedule, namely timing of spring migration across the central Mediterranean sea and moultspeed, the latter gauged from ptilochronological analyses of tail feathers moulted in the Africanwinter quarters. We identified a novel Clockgene locus （Clock region 3） showing polyQ polymorph-ism, which was however not significantly associated with any phenotypic trait. Npas2 allele sizepredicted male （but not female） spring migration date, with males bearing longer alleles migratingsignificantly earlier than those bearing shorter alleles. Crebl allele size significantly predicted male（but not female） moult speed, longer alleles being associated with faster moult. All othergenotype-phenotype associations were statistically non-significant. These findings provide newevidence for a role of candidate genes in modulating the phenology of different circannual activ-ities in long-distance migratory birds, and for the occurrence of sex-specific candidate gene effects.展开更多
基金We thank Yolanda Noordijk for the isolation of DNA from all samples at Wageningen-UR and Elisa Banchi for her work on the genotyping of these samples with the 20 K Infinium SNP array at the Fondazione Edmund MachThis work has been co-funded by the EU seventh Framework Programme by the FruitBreedomics project N°.265582:Integrated Approach for increasing breeding efficiency in fruit tree crops(www.FruitBreedomics.com).
文摘Quantitative trait loci(QTL)mapping approaches rely on the correct ordering of molecular markers along the chromosomes,which can be obtained from genetic linkage maps or a reference genome sequence.For apple(Malus domestica Borkh),the genome sequence v1 and v2 could not meet this need;therefore,a novel approach was devised to develop a dense genetic linkage map,providing the most reliable marker-loci order for the highest possible number of markers.The approach was based on four strategies:(i)the use of multiple full-sib families,(ii)the reduction of missing information through the use of HaploBlocks and alternative calling procedures for single-nucleotide polymorphism(SNP)markers,(iii)the construction of a single backcross-type data set including all families,and(iv)a two-step map generation procedure based on the sequential inclusion of markers.The map comprises 15417 SNP markers,clustered in 3 K HaploBlock markers spanning 1267 cM,with an average distance between adjacent markers of 0.37 cM and a maximum distance of 3.29 cM.Moreover,chromosome 5 was oriented according to its homoeologous chromosome 10.This map was useful to improve the apple genome sequence,design the Axiom Apple 480 K SNP array and perform multifamily-based QTL studies.Its collinearity with the genome sequences v1 and v3 are reported.To our knowledge,this is the shortest published SNP map in apple,while including the largest number of markers,families and individuals.This result validates our methodology,proving its value for the construction of integrated linkage maps for any outbreeding species.
文摘Plant responses to drought are regulated by complex genetic and epigenetic networks leading to rapid reprogramming of plant growth, miRNAs have been widely indicated as key players in the regulation of growth and development. The role of miRNAs in drought response was investigated in young leaves of Brachypodium dis- tachyon, a drought-tolerant monocot model species. Adopting an in vivo drought assay, shown to cause a dramatic reduction in leaf size, mostly due to reduced cell expansion, small RNA libraries were produced from proliferating and expanding leaf cells. Next-generation sequencing data were analyzed using an in-house bioinformatics pipeline allowing the identification of 66 annotated miRNA genes and 122 new high confidence predictions greatly expand- ing the number of known Brachypodium miRNAs. In addition, we identified four TAS3 loci and a large number of siRNA-producing loci that show characteristics suggesting that they may represent young miRNA genes. Most miR- NAs showed a high expression level, consistent with their involvement in early leaf development and cell identity. Proliferating and expanding leaf cells respond differently to drought treatment and differential expression analyses suggest novel evidence for an miRNA regulatory network controlling cell division in both normal and stressed condi-tions and demonstrate that drought trigger a genetic reprogramming of leaf growth in which miRNAs are deeply involved.
文摘The timing of major life-history events, such as migration and moult, is set by endogenous circa-dian and circannual clocks, that have been well characterized at the molecular level. Conversely,the genetic sources of variation in phenology and in other behavioral traits have been sparsely ad-dressed. It has been proposed that inter-individual variability in the timing of seasonal events mayarise from allelic polymorphism at phenological candidate genes involved in the signaling cascadeof the endogenous clocks. In this study of a long-distance migratory passerine bird, the willowwarbler Phylloscopus trochilus, we investigated whether allelic variation at 5 polymorphic loci of 4candidate genes （Adcyapl, Clock, Crebl, and Npas2）, predicted 2 major components of the annualschedule, namely timing of spring migration across the central Mediterranean sea and moultspeed, the latter gauged from ptilochronological analyses of tail feathers moulted in the Africanwinter quarters. We identified a novel Clockgene locus （Clock region 3） showing polyQ polymorph-ism, which was however not significantly associated with any phenotypic trait. Npas2 allele sizepredicted male （but not female） spring migration date, with males bearing longer alleles migratingsignificantly earlier than those bearing shorter alleles. Crebl allele size significantly predicted male（but not female） moult speed, longer alleles being associated with faster moult. All othergenotype-phenotype associations were statistically non-significant. These findings provide newevidence for a role of candidate genes in modulating the phenology of different circannual activ-ities in long-distance migratory birds, and for the occurrence of sex-specific candidate gene effects.
