Genotyping by Target Sequencing(GBTS)technology,known for its flexibility,high efficiency,high throughput,and low cost,has been increasingly employed in molecular breeding.However,there is still limited study on the d...Genotyping by Target Sequencing(GBTS)technology,known for its flexibility,high efficiency,high throughput,and low cost,has been increasingly employed in molecular breeding.However,there is still limited study on the design and development of high-throughput genotyping tools in watermelon.In this study,we identified 112000 high quality SNPs by analyzing the resequencing data of 43 cultivated watermelon accessions.11921 and 6094 SNPs were selected for developing two sets of watermelon liquid-phase chips with different marker densities,named Watermelon 10K and 5K,respectively.Furthermore,the SNPs and Indels of most mapped gene/QTLs for many agronomic important traits in watermelon were also integrated into the two chips for foreground selection.These chips have been tested using GBTS technology in various applications in watermelon.The genotyping of 76 accessions by Watermelon 5K liquid-phase chip showed an average detection rate of 99.28%and 81.78%for cultivated and wild watermelon accessions,respectively.This provided enough markers information for GWAS and two significant QTLs,ssc1.1 and ssc1.2,associated with soluble sugar content were detected.Furthermore,BSA-seq analysis for non-lobed leaf and dwarf traits were validated by liquid-phase chips,and the candidate region was consistent with our previous studies.Additionally,we precisely introduced the Cldw1 and Clbl genes into an elite inbred line WT2 using Watermelon 5K for assisted selection,resulting in the development of three new germplasm with good plant architecture.As a high-throughput genotyping liquid-phase SNP array,the Watermelon 10K and 5K chips will greatly facilitate functional studies and molecular breeding in watermelon.展开更多
A rice mutant with Yaponica 9522 cultivar background Oryza sativa extraordinary glume 1 （Oseg 1） was identified from the M2 mutant pool mutagenized by ^60Co γ-ray. Compared with wild type plants, Oseg 1 developed l...A rice mutant with Yaponica 9522 cultivar background Oryza sativa extraordinary glume 1 （Oseg 1） was identified from the M2 mutant pool mutagenized by ^60Co γ-ray. Compared with wild type plants, Oseg 1 developed longer empty glumes and rudimentary glumes. In some Oseg 1 mutants, the number of stamens of flowers was reduced and leaf-like lodicules occurred, and excessive lemma/palea-like organ could be observed in some mutant spikelets. This indicated that OsEG1 could regulate the development of rudimentary glumes, empty glumes, lemma/palea, lodicules, and stamens. Genetic analysis indicated that Oseg 1 came from a single recessive genetic locus. To clone OsEG1 gene, F2 population was constructed by a cross between Oseg 1 （Japonica） and Guangluai4 （Indica）. Using map-based cloning approach, OsEG1 was mapped on chromosome 4, between INDEL marker OS407 and WHM0466 with genetic distance of 2.0 cm and 1.0 cm, respectively. These results are useful for further cloning and functional analysis of the OsEG1 gene.展开更多
To identify genetic loci controlling grain weight, an elite indica rice variety, Baodali, with large grains was identified and used in this study. Its derived F2, F3 and BC2 F2 with another japonica rice variety Zhong...To identify genetic loci controlling grain weight, an elite indica rice variety, Baodali, with large grains was identified and used in this study. Its derived F2, F3 and BC2 F2 with another japonica rice variety Zhonghua 11 were used as mapping populations. Linkage analyses demonstrated that two genes controlling grain weight, designated as GW3 and GW6, were mapped to chromosome 3 and chromosome 6, respectively. Fine mapping delimited GW3 to a 122 kb physical distance between two sequence tagged site markers （WGWt6 and WGW19） containing 16 open reading frames annotated by The Institute for Genomic Research （http：//www.tigr.org）. GW6 was further mapped between two simple sequence repeat markers （RM7179 and RM3187）. These results are useful for both marker assisted selection of grain weight, and for further cloning of GW genes, which will contribute to the dissection of the molecular mechanism underlying grain weight in rice.展开更多
基金supported by the National Natural Science Foundation of China(Grant Nos.32172602,32472739)the Major Science and Technology Project of Henan Province(Grant No.221100110400)+3 种基金the Funding of Joint Research on Agricultural Varietie Improvement of Henan Province(Grant No.2022010503)the Natural Science Foundation of Henan(Grant No.242300421030)the Key Scientifc and Technological Project of Henan Province(Grant Nos.242102111124,242102111115)the Key Research and Development Program of Xinjiang Uygur autonomous region(2023B02017-2).
文摘Genotyping by Target Sequencing(GBTS)technology,known for its flexibility,high efficiency,high throughput,and low cost,has been increasingly employed in molecular breeding.However,there is still limited study on the design and development of high-throughput genotyping tools in watermelon.In this study,we identified 112000 high quality SNPs by analyzing the resequencing data of 43 cultivated watermelon accessions.11921 and 6094 SNPs were selected for developing two sets of watermelon liquid-phase chips with different marker densities,named Watermelon 10K and 5K,respectively.Furthermore,the SNPs and Indels of most mapped gene/QTLs for many agronomic important traits in watermelon were also integrated into the two chips for foreground selection.These chips have been tested using GBTS technology in various applications in watermelon.The genotyping of 76 accessions by Watermelon 5K liquid-phase chip showed an average detection rate of 99.28%and 81.78%for cultivated and wild watermelon accessions,respectively.This provided enough markers information for GWAS and two significant QTLs,ssc1.1 and ssc1.2,associated with soluble sugar content were detected.Furthermore,BSA-seq analysis for non-lobed leaf and dwarf traits were validated by liquid-phase chips,and the candidate region was consistent with our previous studies.Additionally,we precisely introduced the Cldw1 and Clbl genes into an elite inbred line WT2 using Watermelon 5K for assisted selection,resulting in the development of three new germplasm with good plant architecture.As a high-throughput genotyping liquid-phase SNP array,the Watermelon 10K and 5K chips will greatly facilitate functional studies and molecular breeding in watermelon.
基金Project supported by the National Key Basic Research Development Program of the Ministry of Science and Technology of China(Grant Nos.2001CB109002,2005CB120802)the National High-Techhology Research and Development Program of China(Grant No.2005AA2710330)+2 种基金the Science Foundation of Shanghai Municipal Commission of Science and Technology(Grant Nos.03JC14061,03DJ14016)the Program for New Century Excellent Talents in University(Grant No.NCET-040403)the Shuguang Plan of Shanghai Education Development Foundation(Grant No.04SG15)
文摘A rice mutant with Yaponica 9522 cultivar background Oryza sativa extraordinary glume 1 （Oseg 1） was identified from the M2 mutant pool mutagenized by ^60Co γ-ray. Compared with wild type plants, Oseg 1 developed longer empty glumes and rudimentary glumes. In some Oseg 1 mutants, the number of stamens of flowers was reduced and leaf-like lodicules occurred, and excessive lemma/palea-like organ could be observed in some mutant spikelets. This indicated that OsEG1 could regulate the development of rudimentary glumes, empty glumes, lemma/palea, lodicules, and stamens. Genetic analysis indicated that Oseg 1 came from a single recessive genetic locus. To clone OsEG1 gene, F2 population was constructed by a cross between Oseg 1 （Japonica） and Guangluai4 （Indica）. Using map-based cloning approach, OsEG1 was mapped on chromosome 4, between INDEL marker OS407 and WHM0466 with genetic distance of 2.0 cm and 1.0 cm, respectively. These results are useful for further cloning and functional analysis of the OsEG1 gene.
基金Supported by the National Natural Science Foundation of China (30771317)the State Key Basic Research and Development Plan of China(2005CB120807).
文摘To identify genetic loci controlling grain weight, an elite indica rice variety, Baodali, with large grains was identified and used in this study. Its derived F2, F3 and BC2 F2 with another japonica rice variety Zhonghua 11 were used as mapping populations. Linkage analyses demonstrated that two genes controlling grain weight, designated as GW3 and GW6, were mapped to chromosome 3 and chromosome 6, respectively. Fine mapping delimited GW3 to a 122 kb physical distance between two sequence tagged site markers （WGWt6 and WGW19） containing 16 open reading frames annotated by The Institute for Genomic Research （http：//www.tigr.org）. GW6 was further mapped between two simple sequence repeat markers （RM7179 and RM3187）. These results are useful for both marker assisted selection of grain weight, and for further cloning of GW genes, which will contribute to the dissection of the molecular mechanism underlying grain weight in rice.
