Pyrus pyrifolia,commonly known as sand pear,is a key economic fruit tree in temperate regions that possesses highly diverse germplasm resources for pear quality improvement.However,research on the relationship between...Pyrus pyrifolia,commonly known as sand pear,is a key economic fruit tree in temperate regions that possesses highly diverse germplasm resources for pear quality improvement.However,research on the relationship between resistance and fruit quality traits in the breeding of fruit species like pear is limited.Pan-transcriptomes effectively capture genetic information from coding regions and reflect variations in gene expression between individuals.Here,we constructed a pan-transcriptome based on 506 samples from different tissues of sand pear,and explored the intrinsic relationships among phenotypes and the selection for disease resistance during improvement based on expression presence/absence variations(eP AVs).The pan-transcriptome in this study contains 156,744 transcripts,among which the novel transcripts showed significant enrichment in the defense response.Interestingly,disease resistance genes are highly expressed in landraces of pear but have been selected against during the improvement of this perennial tree species.We found that the genetically diverse landraces can be divided into two subgroups and inferred that they have undergone different dispersal processes.Through co-expression network analysis,we confirmed that the formation of stone cells in pears,the synthesis of fruit anthocyanins,and the ability to resist stress are interrelated.They are jointly regulated by several modules,and the expression of regulatory genes has significant correlations with these three processes.Moreover,we identified candidate genes such as HKL1 that may affect sugar content and are missing from the reference genome.This study provides insights into the associations between complex fruit traits,while providing a database resource for pear disease resistance and fruit quality breeding.展开更多
Tomato(Solanum lycopersicum) stress resistance and fruit total soluble solid(TSS) content have changed dramatically during selective breeding, and transcriptome variation has played a critical role in this rewiring. H...Tomato(Solanum lycopersicum) stress resistance and fruit total soluble solid(TSS) content have changed dramatically during selective breeding, and transcriptome variation has played a critical role in this rewiring. However, the single tomato reference genome impedes characterization of whole-transcriptome variation during domestication and breeding at the population level. Here, we constructed a pan-transcriptome of orange-stage tomato fruit, and investigated global expression presence/absence variation(e PAV) and differentially expressed genes(DEGs) based on RNA sequencing(RNA-seq) data from 399 tomato accessions. A total of 7 181 genes absent from the reference genome were identified, 6 122 of which were e PAV genes during tomato domestication and breeding including resistance genes such as late blight resistance gene PIM_DN29746_c0_g3_i1 and peroxidase P7-like gene PIM_DN30274_c0_g2_i1. In addition, 3 629 genes were significantly differentially expressed during tomato selection, among which 19 genes were associated with the reduced fruit TSS content of modern tomato cultivars, including LIN5, TIV1, and seven novel sugar transporter genes. Our results indicate that natural and artificial selection greatly shaped the tomato transcriptome, thereby altering the fruit TSS content and resistance to abiotic and biotic stresses.展开更多
基金supported by the National Science Foundation of China(32230097)the National Key Research and Development Program of China(2022YFD1200503)+2 种基金the earmarked fund for China Agriculture Research System(CARS-28)the earmarked fund for Jiangsu Agricultural Industry Technology System(JATS[2023]412)the Natural Science Foundation of Jiangsu Province for Young Scholar,China(BK20221010)。
文摘Pyrus pyrifolia,commonly known as sand pear,is a key economic fruit tree in temperate regions that possesses highly diverse germplasm resources for pear quality improvement.However,research on the relationship between resistance and fruit quality traits in the breeding of fruit species like pear is limited.Pan-transcriptomes effectively capture genetic information from coding regions and reflect variations in gene expression between individuals.Here,we constructed a pan-transcriptome based on 506 samples from different tissues of sand pear,and explored the intrinsic relationships among phenotypes and the selection for disease resistance during improvement based on expression presence/absence variations(eP AVs).The pan-transcriptome in this study contains 156,744 transcripts,among which the novel transcripts showed significant enrichment in the defense response.Interestingly,disease resistance genes are highly expressed in landraces of pear but have been selected against during the improvement of this perennial tree species.We found that the genetically diverse landraces can be divided into two subgroups and inferred that they have undergone different dispersal processes.Through co-expression network analysis,we confirmed that the formation of stone cells in pears,the synthesis of fruit anthocyanins,and the ability to resist stress are interrelated.They are jointly regulated by several modules,and the expression of regulatory genes has significant correlations with these three processes.Moreover,we identified candidate genes such as HKL1 that may affect sugar content and are missing from the reference genome.This study provides insights into the associations between complex fruit traits,while providing a database resource for pear disease resistance and fruit quality breeding.
基金supported by the Agricultural Science and Technology Innovation Program (ASTIP-CAAS)the National Natural Science Foundation of China (31601360)the 13th Five-Year Plan Vegetable Breeding Program of Sichuan Province, China (2016NYZ0033)
文摘Tomato(Solanum lycopersicum) stress resistance and fruit total soluble solid(TSS) content have changed dramatically during selective breeding, and transcriptome variation has played a critical role in this rewiring. However, the single tomato reference genome impedes characterization of whole-transcriptome variation during domestication and breeding at the population level. Here, we constructed a pan-transcriptome of orange-stage tomato fruit, and investigated global expression presence/absence variation(e PAV) and differentially expressed genes(DEGs) based on RNA sequencing(RNA-seq) data from 399 tomato accessions. A total of 7 181 genes absent from the reference genome were identified, 6 122 of which were e PAV genes during tomato domestication and breeding including resistance genes such as late blight resistance gene PIM_DN29746_c0_g3_i1 and peroxidase P7-like gene PIM_DN30274_c0_g2_i1. In addition, 3 629 genes were significantly differentially expressed during tomato selection, among which 19 genes were associated with the reduced fruit TSS content of modern tomato cultivars, including LIN5, TIV1, and seven novel sugar transporter genes. Our results indicate that natural and artificial selection greatly shaped the tomato transcriptome, thereby altering the fruit TSS content and resistance to abiotic and biotic stresses.
