小麦—非洲黑麦抗性新种质的分子细胞遗传学鉴定
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摘要
黑麦属（Secale L.，染色体组为R，2n=14）属禾本科（Poaccae）小麦族（Triticeae），是小麦的三级基因库（tertiary gene poo1）。黑麦属物种中蕴藏着丰富的遗传变异,含有与高蛋白含量、高赖氨酸含量、抗病、抗穗发芽、抗旱、抗寒以及其他优异农艺性状和生物化学性状相关的重要基因，是改良普通小麦的重要外源基因供体，但目前小麦育种中利用的黑麦属种质资源主要集中在栽培黑麦上，对野生黑麦的利用还较少。非洲黑麦（Secale africanum Stapf，R~(afr)R~(afr)）属于黑麦属多年生野生黑麦重要一员，主要分布在南非，是濒临灭绝的物种，表现为矮杆和对多种病害具有优异的抗性，因而十分有必要对这一珍贵资源开展研究与利用工作。本研究主要包括：黑麦染色体特异分子标记的开发、一系列小麦-非洲黑麦渐渗系材料的分子细胞学鉴定、非洲黑麦染色体在小麦背景下的抗病性及农艺性状研究以及非洲黑麦和栽培黑麦的多角度差异比较分析。研究结果如下：
1.新的黑麦染色体特异分子标记的开发与应用：（1）利用490对引物开发黑麦染色体特异分子标记，包括138对PLUG（PCR-based landmark unique gene）引物、258对EST-SSR（Expressed sequences tags-Simple sequence repeats）引物、38对STS（Sequence-taged site）引物和56对COS（conserved orthologous set）引物，共获得黑麦染色体特异标记97个，覆盖1R-7R染色体。（2）通过C带、基因组原位杂交（GISH）和荧光原位杂交（FISH）鉴定小麦–非洲黑麦渐渗系材料，并证实，新开发的分子标记可有效跟踪小麦背景中的非洲黑麦染色质。（3）利用已报道的黑麦基因组特异分子标记和本研究新开发的黑麦染色体特异分子标记，对小麦–非洲黑麦高代渐渗系材料进行初步筛选，发现小麦–非洲黑麦高代渐渗系中，出现频率最高的染色体依次是1R~(afr)、6R~(afr)和2R~(afr)。
2.小麦–非洲黑麦1R~(afr)渐渗系材料的鉴定及对黑麦1R染色体进化规律的探讨：（1）在小麦–非洲黑麦1R~(afr)渐渗系中，通过C带和原位杂交鉴定获得小麦–非洲黑麦1R~(afr)附加系、1R~(afr)(1D)代换系、T1BL.1R~(afr)S易位系、T1DS.1R~(afr)L易位系及1R~(afr)L端体等材料。抗性分析表明1R~(afr)S上含有条抗条锈病基因；（2）进一步利用栽培黑麦1BS.1RL易位和1RL端体等材料及本研究鉴定的非洲黑麦1R~(afr)渐渗系材料，将新开发的15个1R染色体特异分子标记定位到1R&1R~(afr)染色体臂。结合已报道的14个1R染色体臂分子标记，研究了这些标记在栽培黑麦1R和非洲黑麦1R~(afr)上的扩增情况。（3）分别从细胞学、分子标记及单基因序列分析等角度进行研究，发现栽培黑麦1R染色体与非洲黑麦1R~(afr)染色体相比，表现为端部高度重复序列增多、微卫星聚集、基因拷贝数增多等变化，而这些变化可能出现在黑麦属基因组进化与栽培化进程中。
3.新型小麦–非洲黑麦2R~(afr)渐渗系的分子细胞遗传学鉴定及农艺性状分析：（1）利用C带、原位杂交和分子标记辅助分析方法，在MY11与硬粒小麦–非洲黑麦双二倍体杂交F6代渐渗系材料中，鉴定了一个稳定的育性极好的2R~(afr)(2D)代换系LF24。通过对小麦、非洲黑麦和LF24接种条锈生理小种，发现LF24中抗条锈病特性来自非洲黑麦2R~(afr)染色体。（2）通过对LF24与MY11杂交后代渐渗系材料进行GISH和FISH分析鉴定，获得T2DL.2R~(afr)S二体易位系、T2DS.2R~(afr)L二体易位系、单2R~(afr)S或单2R~(afr)L附加系等一系列小麦–非洲黑麦2R~(afr)渐渗系。（3）结合C带、GISH、FISH以及分子标记分析，表明非洲黑麦2R~(afr)染色体与栽培黑麦2R染色体相比，存在异染色质减少、端部高度重复序列减少或变化、端部区域删除或重组等基因组改变。（4）通过抗性和农艺性状数据分析，将抗条锈基因及矮秆基因定位在2R~(afr)L染色体臂；通过与代换系和2R~(afr)L株系进行农艺性状比较，发现2R~(afr)S明显具有对产量相关性状的正向作用，如增加穗长、小穗数、千粒重。
4.新型小麦–非洲黑麦6R~(afr)(6D)代换系的鉴定及6R~(afr)上Sec2位点的研究：（1）在小麦–非洲黑麦渐渗系材料中，获得一个稳定株系HH41，分子细胞学分析表明HH41为小麦–非洲黑麦6R~(afr)(6D)代换系。抗性分析表明，HH41上优异的高抗条锈病和中抗白粉病特性可能来自非洲黑麦6R~(afr)染色体。（2）GISH、FISH及分子标记分析表明非洲黑麦6R~(afr)染色体与栽培黑麦6R染色体存在明显多态性。（3）通过SDS-PAGE（Sodium dodecyl sulfate-Polyacrylamide gel electrophoresis）电泳和75K γ-secalin基因特异分子标记分析，将编码75K γ-secalin的Sec2位点定位到非洲黑麦6R~(afr)(6D)代换系。通过克隆、测序和序列比对分析，证实来自6R~(afr)染色体的75K γ-secalin基因序列与已报道的75K γ-secalin基因序列相似度极高。（4）结合已报道的75K γ-secalin基因序列进行聚类分析，表明来自非洲黑麦的序列可以聚为一类，而来自栽培黑麦的序列可以聚为另一类，研究结果发现非洲黑麦与森林黑麦亲缘关系较近，而且栽培黑麦75K γ-secalin基因序列比野生物种序列75Kγ-secalin基因变异幅度大。
Genus Secale (Secale L.,2n=2x=14, RR) belongs to Poaceae (syn. Gramineae), inthe tribe Triticeae, and is a member of tertiary gene pool of bread wheat. It constitutes avast source of genetic diversity and is an important source of genes associated with highprotein content, high lysine, resistant to many cereal diseases, sprouting, drought, winterhardiness, and other morphological and biochemical traits that can be used in wheatbreeding program. Studies in Secale are focused on cultivated rye (S. cereale L.), whilerelatively few studies have involved gene transfer from the wild Secale species to wheat.Wild Secale species, Secale africanum Stapf.(R~(afr)R~(afr)), is an important species in genusSecale, widely distributed in southern Africa and now verging on extinction. S.africanum showed short plant height and excellent resistance to wheat diseases, and wasthus essential to conserve the species and study its potential value for wheatimprovement. This study focused on development of a variety of Secale chromosomespecific molecular markers, identification of a series of new wheat–S. africanumintrogression lines by molecular cytogenetic analysis, investigation of the effects ofdisease resistance and agronomic performance of S. africanum chromatin in wheatbackground and comparision of the differences between cultivated rye and S. africanumchromosomes.The research results showed as follows:
1. Development of new Secale chromosome specific molecular markers.(1) A totalof490pairs of primers, including138pairs of PLUG (PCR-based Landmark UniqueGene) primers and258pairs of EST-SSR (Expressed sequences tags-Simple sequencerepeats) primers,38pairs of STS (Sequence-taged site)primers, and56pairs of COS(conserved orthologous set) primers were utilized to develop Secale chromosomespecific molecular markers. Total97chromosome specific molecular markers wereassigned to Secale chromosomes1R-7R.(2) The wheat–S. africanum introgeressionlines were identified by cytological methods including Giemsa C-banding, genomic insitu hybridizaion (GISH) and fluoresence in situ hybridizaion (FISH). Above newlydeveloped Secale specific markers could be used to track S. africanum chromatin inwheat background.(3) Using the reported Secale genome-specific and newly developed chromosome specific markers, we primarily screenned300wheat–S. africanumintrogressed progenies. It was found that chromosome1R~(afr)transmitted with the highestfrequency, while6R~(afr)was the second, and2R~(afr)was followed.
2. Characterization of a set of wheat–S. africanum1R~(afr)introgression linesrevealed1R chromosome evolutionary trend.(1) Wheat–S. africanum chromosome1R~(afr)addition,1R~(afr)(1D) substitution, T1BL.1R~(afr)S and T1DS.1R~(afr)L translocation, and1R~(afr)L monotelocentric addition lines were indentified from a serial of wheat–S.africanum1R~(afr)introgression lines by Giemsa C-banding and in situ hybridization.Disease resistance screening revealed that chromosome1R~(afr)S carried stripe rustresistance gene(s).(2) Fifteen1R specific molecular markers were localized onchromosome arms of cultivated rye1R and S. africanum1R~(afr)by T1BL.1RS andDTA1RL and also the newly identified S. africanum1R~(afr)introgression lines. Combinedthe reported fourteen1R specific molecular markers, we studied the amplificationpattern between S. cereale chromosome1R and S. africanum1R~(afr)derivatives.(3)Thecomparison of the cytogenetic analysis, target bands of polymorphic markers andnucleotide sequences of these unigene polymorphic markers suggested that accumulatedtrends of highly repetitive sequences and the satellite sequences, gene duplication andsequence divergence might have occurred among Secale species during its evolutionand domestication.
3. Molecular cytogenetic characterization of new wheat–S. africanum chromosome2R~(afr)introgression lines with novel disease resistance and agronomic performances.(1)A stable, highly fertile wheat–S. africanum2R~(afr)(2D) substitution line LF24was derivedfrom the F6generation of the cross between Mianyang11(MY11) and T. durum-S.africanum amphiploid (YF), which was identified through C-banding, in situhybridization and molecular markers analysis. When inoculated with stripe rust isolatesof wheat, S. africanum and LF24, we found that the stripe rust resistance of LF24wasderived from S. africanum chromosome2R~(afr).(2) Based on the screening of theoffsprings from the crosses between LF24and MY11, the T2DL.2R~(afr)S andT2DS.2R~(afr)L translocations, mono-2R~(afr)S and2R~(afr)L addition lines and other S.africanum chromosome2R~(afr)introgression lines were identified by GISH and FISH.(3)Combined the C-banding, GISH, FISH patterns and molecular marker analysis of S.africanum2R~(afr)with2R from different S. cereale, it was suggested that genomic variation such as telomeric heterochromatin reduction, highly repetitive sequencesreduction or variation, telomeric regions deletion or recombination occured in S.africanum2R~(afr)compared with cultivated2R.(4) Disease resistance and agronomicperformance effects of wheat–S. africanum chromosome2R~(afr)derivatives linesindicated that chromosome2R~(afr)L possessed gene(s) for stripe rust resistance anddwarfing, while the2R~(afr)S translocation line was the most favorable for agronomicperformance when compared with the field performance of the substitution, and2R~(afr)Ltranslocation lines.
4．Molecular cytogenetic characterization of a new wheat–S. africanum6R~(afr)(6D)substitution line and the study of Sec2locus on6R~(afr).(1) After screening the wheat–S.africanum introgression lines, we obtained a stable6R~(afr)(6D) substitution line HH41.The excellent stripe rust and moderate powdery mildew resistance might be originatedfrom S. africanum6R~(afr)chromosome.(2) GISH, FISH pattern, molecular markersrevealed the apparent polymorphism between S. africanum chromosome6R~(afr)andcultivated rye chromosome6R.(3) The SDS-PAGE (Sodium dodecyl sulfate-Polyacrylamide gel electrophoresis) and75K γ-secalin gene specific marker testrevealed that Sec2locus encoding75K γ-secalin was located on6R~(afr)(6D) substitutionline. Molecular cloning and sequence comparison confirmed that the S. africanum6R~(afr)derived Sec2sequences matched well with75K γ-secalin gene sequences.(4)Phylogenetic analysis using the S. africanum Sec2sequences and other reported Secale75K γ-secalin gene sequences indicated that the S. africanum Sec2sequences clusteredinto the same group, while the cultivated rye Sec2clustered in defferent groups. Theresults suggested that there was a close relationship between S. africanum and S.sylvestre, and the S. cereale Sec2showed higher variation than those of wild Secalespecies.
1.新的黑麦染色体特异分子标记的开发与应用：（1）利用490对引物开发黑麦染色体特异分子标记，包括138对PLUG（PCR-based landmark unique gene）引物、258对EST-SSR（Expressed sequences tags-Simple sequence repeats）引物、38对STS（Sequence-taged site）引物和56对COS（conserved orthologous set）引物，共获得黑麦染色体特异标记97个，覆盖1R-7R染色体。（2）通过C带、基因组原位杂交（GISH）和荧光原位杂交（FISH）鉴定小麦–非洲黑麦渐渗系材料，并证实，新开发的分子标记可有效跟踪小麦背景中的非洲黑麦染色质。（3）利用已报道的黑麦基因组特异分子标记和本研究新开发的黑麦染色体特异分子标记，对小麦–非洲黑麦高代渐渗系材料进行初步筛选，发现小麦–非洲黑麦高代渐渗系中，出现频率最高的染色体依次是1R~(afr)、6R~(afr)和2R~(afr)。
2.小麦–非洲黑麦1R~(afr)渐渗系材料的鉴定及对黑麦1R染色体进化规律的探讨：（1）在小麦–非洲黑麦1R~(afr)渐渗系中，通过C带和原位杂交鉴定获得小麦–非洲黑麦1R~(afr)附加系、1R~(afr)(1D)代换系、T1BL.1R~(afr)S易位系、T1DS.1R~(afr)L易位系及1R~(afr)L端体等材料。抗性分析表明1R~(afr)S上含有条抗条锈病基因；（2）进一步利用栽培黑麦1BS.1RL易位和1RL端体等材料及本研究鉴定的非洲黑麦1R~(afr)渐渗系材料，将新开发的15个1R染色体特异分子标记定位到1R&1R~(afr)染色体臂。结合已报道的14个1R染色体臂分子标记，研究了这些标记在栽培黑麦1R和非洲黑麦1R~(afr)上的扩增情况。（3）分别从细胞学、分子标记及单基因序列分析等角度进行研究，发现栽培黑麦1R染色体与非洲黑麦1R~(afr)染色体相比，表现为端部高度重复序列增多、微卫星聚集、基因拷贝数增多等变化，而这些变化可能出现在黑麦属基因组进化与栽培化进程中。
3.新型小麦–非洲黑麦2R~(afr)渐渗系的分子细胞遗传学鉴定及农艺性状分析：（1）利用C带、原位杂交和分子标记辅助分析方法，在MY11与硬粒小麦–非洲黑麦双二倍体杂交F6代渐渗系材料中，鉴定了一个稳定的育性极好的2R~(afr)(2D)代换系LF24。通过对小麦、非洲黑麦和LF24接种条锈生理小种，发现LF24中抗条锈病特性来自非洲黑麦2R~(afr)染色体。（2）通过对LF24与MY11杂交后代渐渗系材料进行GISH和FISH分析鉴定，获得T2DL.2R~(afr)S二体易位系、T2DS.2R~(afr)L二体易位系、单2R~(afr)S或单2R~(afr)L附加系等一系列小麦–非洲黑麦2R~(afr)渐渗系。（3）结合C带、GISH、FISH以及分子标记分析，表明非洲黑麦2R~(afr)染色体与栽培黑麦2R染色体相比，存在异染色质减少、端部高度重复序列减少或变化、端部区域删除或重组等基因组改变。（4）通过抗性和农艺性状数据分析，将抗条锈基因及矮秆基因定位在2R~(afr)L染色体臂；通过与代换系和2R~(afr)L株系进行农艺性状比较，发现2R~(afr)S明显具有对产量相关性状的正向作用，如增加穗长、小穗数、千粒重。
4.新型小麦–非洲黑麦6R~(afr)(6D)代换系的鉴定及6R~(afr)上Sec2位点的研究：（1）在小麦–非洲黑麦渐渗系材料中，获得一个稳定株系HH41，分子细胞学分析表明HH41为小麦–非洲黑麦6R~(afr)(6D)代换系。抗性分析表明，HH41上优异的高抗条锈病和中抗白粉病特性可能来自非洲黑麦6R~(afr)染色体。（2）GISH、FISH及分子标记分析表明非洲黑麦6R~(afr)染色体与栽培黑麦6R染色体存在明显多态性。（3）通过SDS-PAGE（Sodium dodecyl sulfate-Polyacrylamide gel electrophoresis）电泳和75K γ-secalin基因特异分子标记分析，将编码75K γ-secalin的Sec2位点定位到非洲黑麦6R~(afr)(6D)代换系。通过克隆、测序和序列比对分析，证实来自6R~(afr)染色体的75K γ-secalin基因序列与已报道的75K γ-secalin基因序列相似度极高。（4）结合已报道的75K γ-secalin基因序列进行聚类分析，表明来自非洲黑麦的序列可以聚为一类，而来自栽培黑麦的序列可以聚为另一类，研究结果发现非洲黑麦与森林黑麦亲缘关系较近，而且栽培黑麦75K γ-secalin基因序列比野生物种序列75Kγ-secalin基因变异幅度大。
Genus Secale (Secale L.,2n=2x=14, RR) belongs to Poaceae (syn. Gramineae), inthe tribe Triticeae, and is a member of tertiary gene pool of bread wheat. It constitutes avast source of genetic diversity and is an important source of genes associated with highprotein content, high lysine, resistant to many cereal diseases, sprouting, drought, winterhardiness, and other morphological and biochemical traits that can be used in wheatbreeding program. Studies in Secale are focused on cultivated rye (S. cereale L.), whilerelatively few studies have involved gene transfer from the wild Secale species to wheat.Wild Secale species, Secale africanum Stapf.(R~(afr)R~(afr)), is an important species in genusSecale, widely distributed in southern Africa and now verging on extinction. S.africanum showed short plant height and excellent resistance to wheat diseases, and wasthus essential to conserve the species and study its potential value for wheatimprovement. This study focused on development of a variety of Secale chromosomespecific molecular markers, identification of a series of new wheat–S. africanumintrogression lines by molecular cytogenetic analysis, investigation of the effects ofdisease resistance and agronomic performance of S. africanum chromatin in wheatbackground and comparision of the differences between cultivated rye and S. africanumchromosomes.The research results showed as follows:
1. Development of new Secale chromosome specific molecular markers.(1) A totalof490pairs of primers, including138pairs of PLUG (PCR-based Landmark UniqueGene) primers and258pairs of EST-SSR (Expressed sequences tags-Simple sequencerepeats) primers,38pairs of STS (Sequence-taged site)primers, and56pairs of COS(conserved orthologous set) primers were utilized to develop Secale chromosomespecific molecular markers. Total97chromosome specific molecular markers wereassigned to Secale chromosomes1R-7R.(2) The wheat–S. africanum introgeressionlines were identified by cytological methods including Giemsa C-banding, genomic insitu hybridizaion (GISH) and fluoresence in situ hybridizaion (FISH). Above newlydeveloped Secale specific markers could be used to track S. africanum chromatin inwheat background.(3) Using the reported Secale genome-specific and newly developed chromosome specific markers, we primarily screenned300wheat–S. africanumintrogressed progenies. It was found that chromosome1R~(afr)transmitted with the highestfrequency, while6R~(afr)was the second, and2R~(afr)was followed.
2. Characterization of a set of wheat–S. africanum1R~(afr)introgression linesrevealed1R chromosome evolutionary trend.(1) Wheat–S. africanum chromosome1R~(afr)addition,1R~(afr)(1D) substitution, T1BL.1R~(afr)S and T1DS.1R~(afr)L translocation, and1R~(afr)L monotelocentric addition lines were indentified from a serial of wheat–S.africanum1R~(afr)introgression lines by Giemsa C-banding and in situ hybridization.Disease resistance screening revealed that chromosome1R~(afr)S carried stripe rustresistance gene(s).(2) Fifteen1R specific molecular markers were localized onchromosome arms of cultivated rye1R and S. africanum1R~(afr)by T1BL.1RS andDTA1RL and also the newly identified S. africanum1R~(afr)introgression lines. Combinedthe reported fourteen1R specific molecular markers, we studied the amplificationpattern between S. cereale chromosome1R and S. africanum1R~(afr)derivatives.(3)Thecomparison of the cytogenetic analysis, target bands of polymorphic markers andnucleotide sequences of these unigene polymorphic markers suggested that accumulatedtrends of highly repetitive sequences and the satellite sequences, gene duplication andsequence divergence might have occurred among Secale species during its evolutionand domestication.
3. Molecular cytogenetic characterization of new wheat–S. africanum chromosome2R~(afr)introgression lines with novel disease resistance and agronomic performances.(1)A stable, highly fertile wheat–S. africanum2R~(afr)(2D) substitution line LF24was derivedfrom the F6generation of the cross between Mianyang11(MY11) and T. durum-S.africanum amphiploid (YF), which was identified through C-banding, in situhybridization and molecular markers analysis. When inoculated with stripe rust isolatesof wheat, S. africanum and LF24, we found that the stripe rust resistance of LF24wasderived from S. africanum chromosome2R~(afr).(2) Based on the screening of theoffsprings from the crosses between LF24and MY11, the T2DL.2R~(afr)S andT2DS.2R~(afr)L translocations, mono-2R~(afr)S and2R~(afr)L addition lines and other S.africanum chromosome2R~(afr)introgression lines were identified by GISH and FISH.(3)Combined the C-banding, GISH, FISH patterns and molecular marker analysis of S.africanum2R~(afr)with2R from different S. cereale, it was suggested that genomic variation such as telomeric heterochromatin reduction, highly repetitive sequencesreduction or variation, telomeric regions deletion or recombination occured in S.africanum2R~(afr)compared with cultivated2R.(4) Disease resistance and agronomicperformance effects of wheat–S. africanum chromosome2R~(afr)derivatives linesindicated that chromosome2R~(afr)L possessed gene(s) for stripe rust resistance anddwarfing, while the2R~(afr)S translocation line was the most favorable for agronomicperformance when compared with the field performance of the substitution, and2R~(afr)Ltranslocation lines.
4．Molecular cytogenetic characterization of a new wheat–S. africanum6R~(afr)(6D)substitution line and the study of Sec2locus on6R~(afr).(1) After screening the wheat–S.africanum introgression lines, we obtained a stable6R~(afr)(6D) substitution line HH41.The excellent stripe rust and moderate powdery mildew resistance might be originatedfrom S. africanum6R~(afr)chromosome.(2) GISH, FISH pattern, molecular markersrevealed the apparent polymorphism between S. africanum chromosome6R~(afr)andcultivated rye chromosome6R.(3) The SDS-PAGE (Sodium dodecyl sulfate-Polyacrylamide gel electrophoresis) and75K γ-secalin gene specific marker testrevealed that Sec2locus encoding75K γ-secalin was located on6R~(afr)(6D) substitutionline. Molecular cloning and sequence comparison confirmed that the S. africanum6R~(afr)derived Sec2sequences matched well with75K γ-secalin gene sequences.(4)Phylogenetic analysis using the S. africanum Sec2sequences and other reported Secale75K γ-secalin gene sequences indicated that the S. africanum Sec2sequences clusteredinto the same group, while the cultivated rye Sec2clustered in defferent groups. Theresults suggested that there was a close relationship between S. africanum and S.sylvestre, and the S. cereale Sec2showed higher variation than those of wild Secalespecies.
引文
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