In the present study, a set of chromosome segment introgression lines （CSILs） using Gossypium hirsutum L. TM-1 as the recipient parent and G. barbadense Hai7124 as the donor parent were used to explore the genetic b...In the present study, a set of chromosome segment introgression lines （CSILs） using Gossypium hirsutum L. TM-1 as the recipient parent and G. barbadense Hai7124 as the donor parent were used to explore the genetic basis of heterosis for interspecific hybrids. Two sets of F1 populations individually derived from CSILs crossing with both parents were configured to investigate heterotic loci （HL） and substitution effect loci （SL）. A total of 58 HL and 39 SL were identified in 3 years. One stable HL, hLP-A4-3, could be detected in all 3 years. Three HLs, hBS-A8-1, hLP-D6-1, and hSI-D7-11, could be detected in 2 years. Four SLs, sBSoD7- 1, sLP-A8-1, sLP-D7-1, and sLP-D12-1, could be detected in 2 years. HL and SL tended to be distributed in some HL-rich chromosome segments with close positions. Compared with QTL detected in a former study, HL showed little overlap with QTL, indicating that trait phenotype and heterosis might be controlled by different sets of loci. All three forms of genetic effects （partial-, full-, over-dominant） were identified, while the over-dominant effect made the main contribution to heterosis. These results may help lay the foundation for clarifying the heredity mechanism of heterosis in cotton.展开更多
The Y chromosome plays key roles in male fertility and reflects the evolutionary history of paternal lineages.Here,we present a de novo genome assembly of the Hu sheep with the first draft assembly of ovine Y chromoso...The Y chromosome plays key roles in male fertility and reflects the evolutionary history of paternal lineages.Here,we present a de novo genome assembly of the Hu sheep with the first draft assembly of ovine Y chromosome(o MSY),using nanopore sequencing and Hi-C technologies.The o MSY that we generated spans 10.6 Mb from which 775 Y-SNPs were identified by applying a large panel of whole genome sequences from worldwide sheep and wild Iranian mouflons.Three major paternal lineages(HY1a,HY1b and HY2)were defined across domestic sheep,of which HY2 was newly detected.Surprisingly,HY2 forms a monophyletic clade with the Iranian mouflons and is highly divergent from both HY1a and HY1b.Demographic analysis of Y chromosomes,mitochondrial and nuclear genomes confirmed that HY2 and the maternal counterpart of lineage C represented a distinct wild mouflon population in Iran that diverge from the direct ancestor of domestic sheep,the wild mouflons in Southeastern Anatolia.Our results suggest that wild Iranian mouflons had introgressed into domestic sheep and thereby introduced this Iranian mouflon specific lineage carrying HY2 to both East Asian and Africa sheep populations.展开更多
Chromosome segmental introgression lines（ILs）are an effective way to utilize germplasm resources in crops.To improve agronomic traits of wheat cultivar（Triticum aestivum） Shi 4185, four sets of ILs were developed....Chromosome segmental introgression lines（ILs）are an effective way to utilize germplasm resources in crops.To improve agronomic traits of wheat cultivar（Triticum aestivum） Shi 4185, four sets of ILs were developed. The donors were Chinese endemic subspecies accessions Yunnan wheat（T. aestivum ssp. yunnanense） YN3, Tibetan semiwild wheat（T. aestivum ssp. tibetanum） XZ-ZM19450, and Xinjiang wheat（T. aestivum ssp. petropavlovskyi） XJ5, and synthetic wheat HC-XM1620 derived from a cross between T. durum acc. D67.2/P66.270 with Aegilops tauschii acc. 218.Totals of 356, 366, 445 and 457 simple sequence repeat（SSR）markers were polymorphic between Shi 4185 and YN3, XZZM19450, XJ5 and HC-XM1620, respectively. In total, 991 ILs were identified, including 300 derived from YN3, covering 95%of the genome of Shi 4185, 218 from XZ-ZM19450（79%）, 279 from XJ5（97%）, and 194 from HC-ZX1620（84%）. The sizes and locations of each introgression were determined from a consensus SSR linkage map. Using the ILs, 11 putative Resear quantitative trait loci（QTLs） were identified for plant height（PH）, spike length（SL） and grain number per spike（GNS）.Comparative analyses of 24 elite ILs with the parents revealed that the four donor parents could be important resources to improve wheat SL and GNS. Our work offers a case for utilizing endemic landraces for QTL mapping and improvement of wheat cultivars using introgression lines.展开更多
Incomplete lineage sorting and introgression are 2 major and nonexclusive causes of specieslevel non-monophyly.Distinguishing between these 2 processes is notoriously difficult because they can generate similar geneti...Incomplete lineage sorting and introgression are 2 major and nonexclusive causes of specieslevel non-monophyly.Distinguishing between these 2 processes is notoriously difficult because they can generate similar genetic signatures.Previous studies have suggested that 2 closely related duck species,the Chinese spot-billed duck Anas zonorhyncha and the mallard A.platyrhynchosvjere polyphyletically intermixed.Here,we utilized a wide geographical sampling,multilocus data and a coalescent-based model to revisit this system.Our study confirms the finding that Chinese spot-billed ducks and Mallards are not monophyletic.There was no apparent interspecific differentiation across loci except those at the mitochondrial DNA(mtDNA)control region and the Z chromosome(CHD1Z).Based on an isolation-with-migration model and the geographical distribution of lineages,we suggest that both introgression and incomplete lineage sorting might contribute to the observed non-monophyly of the 2 closely related duck species.The mtDNA introgression was asymmetric,with high gene flow from Chinese spot-billed ducks to Mallards and negligible gene flow in the opposite direction.Given that the 2 duck species are phenotypically distinctive but weakly genetically differentiated,future work based on genomescale data is necessary to uncover genomic regions that are involved in divergence,and this work may provide further insights into the evolutionary histories of the 2 species and other waterfowls.展开更多
通过对黄瓜种间杂交后代BC1F4群体进行农艺学和细胞学分析,鉴定筛选出抗枯萎病异源易位植株AT 04。农艺学观察表明,其具有小叶、短果、棕色瘤刺、多分枝的特点,形态上偏向原始亲本野生种Cucum is hystrixChakr.,育性与栽培黄瓜相近。细...通过对黄瓜种间杂交后代BC1F4群体进行农艺学和细胞学分析,鉴定筛选出抗枯萎病异源易位植株AT 04。农艺学观察表明,其具有小叶、短果、棕色瘤刺、多分枝的特点,形态上偏向原始亲本野生种Cucum is hystrixChakr.,育性与栽培黄瓜相近。细胞学研究发现,AT 04在有丝分裂的中后期至少有1对染色体的姊妹染色单体分离明显滞后。在减数分裂终变期,平均每个花粉母细胞有0.2个四价体、0.05个六价体和0.05个八价体,约30%的花粉母细胞中存在拉十字的染色体。在中期Ⅰ,7个二价体出现分组分布现象,主要以3+2+2形式存在,表明其至少经历了4次染色体易位。田间调查和人工接种鉴定均表明,易位植株AT 04及其自交后代和野生种C.hystrix对枯萎病具有较高抗性。展开更多
【目的】利用基因组荧光原位杂交(genomic in situ hybridization,GISH)技术,对黄瓜(Cucumis sativus L.,2n=2x=14)种内两个变种(栽培黄瓜C.sativus var.sativus和野生黄瓜C.sativus var hardwickii)进行中期染色体分析,建立黄瓜变种染...【目的】利用基因组荧光原位杂交(genomic in situ hybridization,GISH)技术,对黄瓜(Cucumis sativus L.,2n=2x=14)种内两个变种(栽培黄瓜C.sativus var.sativus和野生黄瓜C.sativus var hardwickii)进行中期染色体分析,建立黄瓜变种染色体核型的快速分析方法,为黄瓜细胞分子遗传学研究提供基础。【方法】以栽培黄瓜‘9930’和野生黄瓜C.sativus var.hardwickii为材料,利用CTAB法提取栽培黄瓜‘9930’的基因组总DNA,采用缺刻平移法,将栽培黄瓜‘9930’基因组DNA和45S r DNA分别利用地高辛和生物素标记为探针,与栽培黄瓜‘9930’和野生变种C.sativus var.hardwickii的中期染色体进行荧光原位杂交,根据杂交结果显示的栽培黄瓜与野生变种每条染色体GISH荧光带型的不同,结合45S r DNA位点信号特征,区分栽培黄瓜与野生变种的每条染色体,并进行核型分析。【结果】荧光原位杂交结果显示,GISH信号并非平均分布于所有染色体上,而是在不同染色体的特定部位产生独特的信号,且两个变种间中期染色体的GISH信号模式差异显著。在栽培黄瓜‘9930’有丝分裂中期染色体上,除了6号染色体仅在短臂末端和近着丝粒处产生GISH信号外,其他染色体上的GISH信号集中分布于染色体的两端和近着丝粒的一侧或两侧,且每条染色体的信号特征差异明显;45S r DNA信号主要分布于‘9930’的第1、2、3、4和7号染色体的近着丝粒处,有3对强信号和2对弱信号。在野生黄瓜C.sativus var.hardwickii有丝分裂中期染色体上,杂交信号的位置及强弱与栽培黄瓜‘9930’表现明显不同,近着丝粒处均有GISH信号,但仅在第1、2、4和5号染色体的一端产生GISH信号,45S r DNA信号仅出现在第1、2和3号染色体上,表现为第1号染色体上信号极强,第2和3号染色体上信号极微弱。这些结果显示,以栽培黄瓜基因组DNA为探针的荧光原位杂交能反应出两个变种中期染色体独特的信号分布模式,通过信号的分布模式和强弱,结合45S r DNA位点信号的特异分布,可对每条染色体进行清晰地鉴别,并据此建立了两个变种的核型模式。比较前人发表的黄瓜已有重复序列的分布图,发现GISH揭示的信号分布主要位于黄瓜染色体串联重复序列区域。【结论】黄瓜基因组原位杂交能一次性快速显示基因组串联重复序列的分布图,能有效地用于不同黄瓜变种的快速核型分析;同时发现染色体上串联重复序列的分布及强弱在黄瓜变种间表现出明显的分化。展开更多
基金supported by grants from the Shandong Province System of Modern Agriculture Industrial Technology(Cotton industry)the Science and Technology Development Project of Shandong Province (2012GGB01026)the Shandong Agricultural Breeding Project(2010LZ005-01)
文摘In the present study, a set of chromosome segment introgression lines （CSILs） using Gossypium hirsutum L. TM-1 as the recipient parent and G. barbadense Hai7124 as the donor parent were used to explore the genetic basis of heterosis for interspecific hybrids. Two sets of F1 populations individually derived from CSILs crossing with both parents were configured to investigate heterotic loci （HL） and substitution effect loci （SL）. A total of 58 HL and 39 SL were identified in 3 years. One stable HL, hLP-A4-3, could be detected in all 3 years. Three HLs, hBS-A8-1, hLP-D6-1, and hSI-D7-11, could be detected in 2 years. Four SLs, sBSoD7- 1, sLP-A8-1, sLP-D7-1, and sLP-D12-1, could be detected in 2 years. HL and SL tended to be distributed in some HL-rich chromosome segments with close positions. Compared with QTL detected in a former study, HL showed little overlap with QTL, indicating that trait phenotype and heterosis might be controlled by different sets of loci. All three forms of genetic effects （partial-, full-, over-dominant） were identified, while the over-dominant effect made the main contribution to heterosis. These results may help lay the foundation for clarifying the heredity mechanism of heterosis in cotton.
基金supported by the National Natural Science Foundation of China(31822052)the National Thousand Youth Talents Plan,Natural Science Foundation of China(31802027)Natural Science Basic Research Plan in Shaanxi Province of China(2019JQ002)。
文摘The Y chromosome plays key roles in male fertility and reflects the evolutionary history of paternal lineages.Here,we present a de novo genome assembly of the Hu sheep with the first draft assembly of ovine Y chromosome(o MSY),using nanopore sequencing and Hi-C technologies.The o MSY that we generated spans 10.6 Mb from which 775 Y-SNPs were identified by applying a large panel of whole genome sequences from worldwide sheep and wild Iranian mouflons.Three major paternal lineages(HY1a,HY1b and HY2)were defined across domestic sheep,of which HY2 was newly detected.Surprisingly,HY2 forms a monophyletic clade with the Iranian mouflons and is highly divergent from both HY1a and HY1b.Demographic analysis of Y chromosomes,mitochondrial and nuclear genomes confirmed that HY2 and the maternal counterpart of lineage C represented a distinct wild mouflon population in Iran that diverge from the direct ancestor of domestic sheep,the wild mouflons in Southeastern Anatolia.Our results suggest that wild Iranian mouflons had introgressed into domestic sheep and thereby introduced this Iranian mouflon specific lineage carrying HY2 to both East Asian and Africa sheep populations.
基金sponsored by the Ministry of Science and Technology of China(2013BAD01B02)the National Science and Technology Major Project of China(2009ZX08009010)
文摘Chromosome segmental introgression lines（ILs）are an effective way to utilize germplasm resources in crops.To improve agronomic traits of wheat cultivar（Triticum aestivum） Shi 4185, four sets of ILs were developed. The donors were Chinese endemic subspecies accessions Yunnan wheat（T. aestivum ssp. yunnanense） YN3, Tibetan semiwild wheat（T. aestivum ssp. tibetanum） XZ-ZM19450, and Xinjiang wheat（T. aestivum ssp. petropavlovskyi） XJ5, and synthetic wheat HC-XM1620 derived from a cross between T. durum acc. D67.2/P66.270 with Aegilops tauschii acc. 218.Totals of 356, 366, 445 and 457 simple sequence repeat（SSR）markers were polymorphic between Shi 4185 and YN3, XZZM19450, XJ5 and HC-XM1620, respectively. In total, 991 ILs were identified, including 300 derived from YN3, covering 95%of the genome of Shi 4185, 218 from XZ-ZM19450（79%）, 279 from XJ5（97%）, and 194 from HC-ZX1620（84%）. The sizes and locations of each introgression were determined from a consensus SSR linkage map. Using the ILs, 11 putative Resear quantitative trait loci（QTLs） were identified for plant height（PH）, spike length（SL） and grain number per spike（GNS）.Comparative analyses of 24 elite ILs with the parents revealed that the four donor parents could be important resources to improve wheat SL and GNS. Our work offers a case for utilizing endemic landraces for QTL mapping and improvement of wheat cultivars using introgression lines.
基金the National Natural Science Foundation of China(No.31401969,31772480)the Natural Science Foundation of Jiangxi Province(No.20161BAB214158).
文摘Incomplete lineage sorting and introgression are 2 major and nonexclusive causes of specieslevel non-monophyly.Distinguishing between these 2 processes is notoriously difficult because they can generate similar genetic signatures.Previous studies have suggested that 2 closely related duck species,the Chinese spot-billed duck Anas zonorhyncha and the mallard A.platyrhynchosvjere polyphyletically intermixed.Here,we utilized a wide geographical sampling,multilocus data and a coalescent-based model to revisit this system.Our study confirms the finding that Chinese spot-billed ducks and Mallards are not monophyletic.There was no apparent interspecific differentiation across loci except those at the mitochondrial DNA(mtDNA)control region and the Z chromosome(CHD1Z).Based on an isolation-with-migration model and the geographical distribution of lineages,we suggest that both introgression and incomplete lineage sorting might contribute to the observed non-monophyly of the 2 closely related duck species.The mtDNA introgression was asymmetric,with high gene flow from Chinese spot-billed ducks to Mallards and negligible gene flow in the opposite direction.Given that the 2 duck species are phenotypically distinctive but weakly genetically differentiated,future work based on genomescale data is necessary to uncover genomic regions that are involved in divergence,and this work may provide further insights into the evolutionary histories of the 2 species and other waterfowls.
文摘【目的】利用基因组荧光原位杂交(genomic in situ hybridization,GISH)技术,对黄瓜(Cucumis sativus L.,2n=2x=14)种内两个变种(栽培黄瓜C.sativus var.sativus和野生黄瓜C.sativus var hardwickii)进行中期染色体分析,建立黄瓜变种染色体核型的快速分析方法,为黄瓜细胞分子遗传学研究提供基础。【方法】以栽培黄瓜‘9930’和野生黄瓜C.sativus var.hardwickii为材料,利用CTAB法提取栽培黄瓜‘9930’的基因组总DNA,采用缺刻平移法,将栽培黄瓜‘9930’基因组DNA和45S r DNA分别利用地高辛和生物素标记为探针,与栽培黄瓜‘9930’和野生变种C.sativus var.hardwickii的中期染色体进行荧光原位杂交,根据杂交结果显示的栽培黄瓜与野生变种每条染色体GISH荧光带型的不同,结合45S r DNA位点信号特征,区分栽培黄瓜与野生变种的每条染色体,并进行核型分析。【结果】荧光原位杂交结果显示,GISH信号并非平均分布于所有染色体上,而是在不同染色体的特定部位产生独特的信号,且两个变种间中期染色体的GISH信号模式差异显著。在栽培黄瓜‘9930’有丝分裂中期染色体上,除了6号染色体仅在短臂末端和近着丝粒处产生GISH信号外,其他染色体上的GISH信号集中分布于染色体的两端和近着丝粒的一侧或两侧,且每条染色体的信号特征差异明显;45S r DNA信号主要分布于‘9930’的第1、2、3、4和7号染色体的近着丝粒处,有3对强信号和2对弱信号。在野生黄瓜C.sativus var.hardwickii有丝分裂中期染色体上,杂交信号的位置及强弱与栽培黄瓜‘9930’表现明显不同,近着丝粒处均有GISH信号,但仅在第1、2、4和5号染色体的一端产生GISH信号,45S r DNA信号仅出现在第1、2和3号染色体上,表现为第1号染色体上信号极强,第2和3号染色体上信号极微弱。这些结果显示,以栽培黄瓜基因组DNA为探针的荧光原位杂交能反应出两个变种中期染色体独特的信号分布模式,通过信号的分布模式和强弱,结合45S r DNA位点信号的特异分布,可对每条染色体进行清晰地鉴别,并据此建立了两个变种的核型模式。比较前人发表的黄瓜已有重复序列的分布图,发现GISH揭示的信号分布主要位于黄瓜染色体串联重复序列区域。【结论】黄瓜基因组原位杂交能一次性快速显示基因组串联重复序列的分布图,能有效地用于不同黄瓜变种的快速核型分析;同时发现染色体上串联重复序列的分布及强弱在黄瓜变种间表现出明显的分化。
