中国糯玉米的分子系统学研究
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摘要
糯玉米其糯质受隐性突变基因wx控制,wx基因位于第9染色体9.03位置(Maize DB,2002)。糯玉米具有许多优良特性,品质极佳,具有很高的经济价值,是食品、纺织、造纸、酿造、饲料等行业的重要原料。
国内外学者以前一直认为糯玉米为硬粒玉米传入我国后经单基因突变而来;但曾孟潜(1981)研究表明,中国糯玉米具有许多原始性状,并且具有特有的过氧化物同工酶第五带,认为糯玉米系我国原生,其起源可能与Coix属有关;李懋学等(1990)对栽培玉米各类型及大刍草进行了核型分析,结果表明糯玉米核型较为对称更接近于爆裂玉米,而后者是公认的较为原始的玉米类型;黄玉碧等(1997,1998,2002),刘永建等(2005)根据RAPD标记、SSR标记研究结果提出,糯玉米基因组与普通玉米基因存在较大差异,不大可能由普通玉米单基因突变而来,其起源进化问题值得研究。由此可见,糯玉米的起源地点、起源方式至今尚无定论。进一步理清玉米族系统进化关系,进行玉蜀黍属(Zea L.)系统发育重建,澄清糯玉米起源与进化问题,具有重要的理论意义。
本研究以西南地区糯玉米、普通玉米地方种质、栽培玉米各种类型材料及部分玉米野生近缘材料为研究对象,对来自线粒体基因组的nad1基因第2内含子、叶绿体基因组的rpL16内含子、核基因组的glb1基因部分序列、waxy基因部分序列以及核rDNA的ITS区等5个分子标记进行序列测定,并根据所测序列BLAST结果从Genbank中下载了部分同源序列,对玉蜀黍属系统发育关系进行了重建。重点讨论了糯玉米在玉蜀黍属的系统学位置及其与小颖玉米、美洲栽培玉米、中国普通玉米的系统发育关系。利用群体遗传学方法,以近年来发展起来的溯祖模型为理论基础,模拟了糯玉米的群体进化历史,探讨了在糯玉米物种形成、群体进化过程中选择、漂变、生态等因素所起的作用,分析了糯玉米的驯化瓶颈及其对现代玉米育种的意义;采用地理系统发育研究方法,研究了糯玉米的地理起源问题。取得了以下主要研究结果:
1、测定了云南、广西糯玉米材料3份,美洲糯玉米2份及有稃种、甜质型、马齿型、粉质等玉米类型各1份,共9份材料的ITS序列,并比对下载了多年生玉米、二倍体多年生玉米、小颖玉米、墨西哥玉米、美洲栽培玉米等共26个同源性较高的ITS序列,序列分析表明ITS区糯玉米核苷酸多态性远远大于玉蜀黍属内其它种或亚种,发现了两个玉米假基因序列(分别为云南糯玉米四路糯和墨西哥玉米M075);最大简约树表明糯玉米及其中国栽培玉米(其中包括美洲糯玉米923A)形成一个单系分支,而目前公认的栽培玉米祖先小颖玉米、可能祖先薏苡、可能祖先摩擦禾都在
The glutinous endosperm of the waxy corn was controlled by a recessive mutation named wax, which locates in the 9th chromosome. The waxy corn, with many excellent characters, better quality, higher economy value, is the important raw material for food industry, textile, paper-making, micro brew and feedstuff.It was well accepted that the waxy corn was the single gene mutation of the flint corn. Zeng Mengqian (1981) thought that the Chinese waxy corn had many pristine characters as well as the 5th band of the distinct peroxide enzyme, so that the waxy corn was originated in China and perhaps had some relationships with the Coix L.. Li Maoxue (1990) revealed that the karyotype of the waxy corn was more related to pop corn, while the latter was well known as the primordial type. HuangYubi (1997) put forward that the genome of the waxy corn had too much differences from that of the normal maize. Therefore, it was impossible that the waxy corn was mutated from the normal one just by single gene mutation, and it worth to research its origin. It can be seen that the origin place, the origin path of the waxy corn are not obvious till today. To clarify the evolution of the maize family, the origin and evolution of the waxy corn and reconstruct the Zea L. phylogenesis are important to the academic research of maize.Recently molecular systematics makes great progresses and many new theories and methods are applied to confirm the position or trace the origin of plant. In present research normal maize landraces and waxy corn landraces from the Southwest of China, special types of maize cultivar, relatives of maize were collected as experimental materials in this study. At the same time some sequences, which were determined by results of BLASTn were downloaded from GENBANK and were added in our data matrix. Five kinds of molecular markers including the 2nd intron of the mitochondrion genome, the intron rpL\6 of the chloroplast genome, and the glb1 gene sequence, the waxy gene sequence and the rDNA ITS region of the nucleus genosome were used to the waxy corn systematic study. This study reconstructed the Zea genus phylogenesis and emphasized on the systematic position of the waxy corn and the phylogenesis relationship between the waxy corn and
Zmays.ssp.parviglumis、 the America cultivated maize and the Chinese normal maize. Based on the coalescent model, the population evolution history of the waxy corn was simulated and selection, gene flow, ecology factors in the speciation of the waxy corn and the population evolution were discussed in details. The domestication bottleneck of the waxy corn and its sense to modern maize breeding were also discussed. Furthermore, the phylogeography method was adopted to study the geographical origin of the waxy corn. And the following results are received:1. The ITS sequences of 3 waxy corn landraces, 2 America waxy mutants, and 4 special types of maize cultivar were sequenced. 26 sequences downloaded from GENBANK were added into the data matrix. The sequence analysis showed that the nucleotide polymorphisms of ITS of the waxy corn were more than the other species or subspecies in Zea L. Two Zea pseudogenes were found in the study. The MP tree showed that the Chinese maize (including waxy corn) has formed much independent clade. But the possible ancestors werer not in the same clad. It was indicated that the waxy corn has special origin and evolution path.2. Twenty glb1 sequences including 11 waxy corn landraces, 6 special types of cultivated maize and 3 relatives were sequenced. With 23 sequences downloaded from GENBANK 20 sequences were analyzed .The results showed that the nucleotide polymorphism of waxy corn was the most one among all taxa. The fixed differences and shared polymorphisms between all taxa sampled displayed that the waxy corn, Z.mays.ssp.parviglumis have less divergent time than and are more relative to normal maize (especially the America cultivated maize and Chinese normal maize). The waxy corn has obvious divergence to Zperennis, Z.diploperennis and Z. luxurians but is less relative to them than Z.mays.ssp.parviglumis, Z.mays.ssp.mexicana and cultivated maize. It was likely that the relationships between the waxy corn, Zmays.ssp.parviglumis and the normal cultivated maize are much close. But the possibility that the waxy corn wass mutated by the normal maize through single gene mutation was much little. It can be concluded that Zmays.ssp.parviglumis is possibly the ancestor of the cultivated corn and the waxy corn or Z.mays.ssp.parviglumis has the same ancestor with the waxy corn.3. The partial sequences of waxy gene of 23 materials including the waxy corn and the normal corn were sequenced. 40 sequences were downloaded from Genbank. Sequences
comparison, Tajiama'D test, Fu and Li's D* and Fu and Li's F* all indicated that the locus evolution of the waxy corn and the others is different, the waxy locus was effected by selection directly and its nucleotide polymorphisms decreased obviously which was related to the traditional eating habit of dwellers in the southwestern China. This is the first proved locus of the maize controlling the starth parthway which is related to artificial selection directly.4. The analysis of rpL16 sequence, ITS region and waxy gene all indicated that the genetic differentiation between coxi and waxy corn are so big that the waxy corn has no possibility of being origined from coix.5. According to phylogeography, the partial sequences of waxy gene of 77 materials including 43 waxy corn landraces and 34 non-waxy corn landraces were compared. Ten haplotypes were found in the 77 sampled sequences from different regions. Using most parsimony method and taking coix as outgroup we constructed the rooted haplotype tree. The geographical origin of the waxy corn is determined according to the topology of the MP tree, variation patterns of haplotypes and the geographical distribution of the originality haplotype. The results indicated that the waxy corn was originated from the southwest of china, exactly in partial special ecological area of the common boundary of Yunnan、 Guangxi and Guizhou, which locates between 23 ° N~25° N, nearby 105° E.6. The 2nd intron of nad1 of the mitochondrion genome and the rpL16 of the chloroplast genome were sequenced. The systematic value of the two cytoplasmic DNA sequences in maize genes evolution was clarified. It is considered that The 2nd intron of nadl change faster than rpL16 and contain more systematical information for the recostruction of Zea genus.
国内外学者以前一直认为糯玉米为硬粒玉米传入我国后经单基因突变而来;但曾孟潜(1981)研究表明,中国糯玉米具有许多原始性状,并且具有特有的过氧化物同工酶第五带,认为糯玉米系我国原生,其起源可能与Coix属有关;李懋学等(1990)对栽培玉米各类型及大刍草进行了核型分析,结果表明糯玉米核型较为对称更接近于爆裂玉米,而后者是公认的较为原始的玉米类型;黄玉碧等(1997,1998,2002),刘永建等(2005)根据RAPD标记、SSR标记研究结果提出,糯玉米基因组与普通玉米基因存在较大差异,不大可能由普通玉米单基因突变而来,其起源进化问题值得研究。由此可见,糯玉米的起源地点、起源方式至今尚无定论。进一步理清玉米族系统进化关系,进行玉蜀黍属(Zea L.)系统发育重建,澄清糯玉米起源与进化问题,具有重要的理论意义。
本研究以西南地区糯玉米、普通玉米地方种质、栽培玉米各种类型材料及部分玉米野生近缘材料为研究对象,对来自线粒体基因组的nad1基因第2内含子、叶绿体基因组的rpL16内含子、核基因组的glb1基因部分序列、waxy基因部分序列以及核rDNA的ITS区等5个分子标记进行序列测定,并根据所测序列BLAST结果从Genbank中下载了部分同源序列,对玉蜀黍属系统发育关系进行了重建。重点讨论了糯玉米在玉蜀黍属的系统学位置及其与小颖玉米、美洲栽培玉米、中国普通玉米的系统发育关系。利用群体遗传学方法,以近年来发展起来的溯祖模型为理论基础,模拟了糯玉米的群体进化历史,探讨了在糯玉米物种形成、群体进化过程中选择、漂变、生态等因素所起的作用,分析了糯玉米的驯化瓶颈及其对现代玉米育种的意义;采用地理系统发育研究方法,研究了糯玉米的地理起源问题。取得了以下主要研究结果:
1、测定了云南、广西糯玉米材料3份,美洲糯玉米2份及有稃种、甜质型、马齿型、粉质等玉米类型各1份,共9份材料的ITS序列,并比对下载了多年生玉米、二倍体多年生玉米、小颖玉米、墨西哥玉米、美洲栽培玉米等共26个同源性较高的ITS序列,序列分析表明ITS区糯玉米核苷酸多态性远远大于玉蜀黍属内其它种或亚种,发现了两个玉米假基因序列(分别为云南糯玉米四路糯和墨西哥玉米M075);最大简约树表明糯玉米及其中国栽培玉米(其中包括美洲糯玉米923A)形成一个单系分支,而目前公认的栽培玉米祖先小颖玉米、可能祖先薏苡、可能祖先摩擦禾都在
The glutinous endosperm of the waxy corn was controlled by a recessive mutation named wax, which locates in the 9th chromosome. The waxy corn, with many excellent characters, better quality, higher economy value, is the important raw material for food industry, textile, paper-making, micro brew and feedstuff.It was well accepted that the waxy corn was the single gene mutation of the flint corn. Zeng Mengqian (1981) thought that the Chinese waxy corn had many pristine characters as well as the 5th band of the distinct peroxide enzyme, so that the waxy corn was originated in China and perhaps had some relationships with the Coix L.. Li Maoxue (1990) revealed that the karyotype of the waxy corn was more related to pop corn, while the latter was well known as the primordial type. HuangYubi (1997) put forward that the genome of the waxy corn had too much differences from that of the normal maize. Therefore, it was impossible that the waxy corn was mutated from the normal one just by single gene mutation, and it worth to research its origin. It can be seen that the origin place, the origin path of the waxy corn are not obvious till today. To clarify the evolution of the maize family, the origin and evolution of the waxy corn and reconstruct the Zea L. phylogenesis are important to the academic research of maize.Recently molecular systematics makes great progresses and many new theories and methods are applied to confirm the position or trace the origin of plant. In present research normal maize landraces and waxy corn landraces from the Southwest of China, special types of maize cultivar, relatives of maize were collected as experimental materials in this study. At the same time some sequences, which were determined by results of BLASTn were downloaded from GENBANK and were added in our data matrix. Five kinds of molecular markers including the 2nd intron of the mitochondrion genome, the intron rpL\6 of the chloroplast genome, and the glb1 gene sequence, the waxy gene sequence and the rDNA ITS region of the nucleus genosome were used to the waxy corn systematic study. This study reconstructed the Zea genus phylogenesis and emphasized on the systematic position of the waxy corn and the phylogenesis relationship between the waxy corn and
Zmays.ssp.parviglumis、 the America cultivated maize and the Chinese normal maize. Based on the coalescent model, the population evolution history of the waxy corn was simulated and selection, gene flow, ecology factors in the speciation of the waxy corn and the population evolution were discussed in details. The domestication bottleneck of the waxy corn and its sense to modern maize breeding were also discussed. Furthermore, the phylogeography method was adopted to study the geographical origin of the waxy corn. And the following results are received:1. The ITS sequences of 3 waxy corn landraces, 2 America waxy mutants, and 4 special types of maize cultivar were sequenced. 26 sequences downloaded from GENBANK were added into the data matrix. The sequence analysis showed that the nucleotide polymorphisms of ITS of the waxy corn were more than the other species or subspecies in Zea L. Two Zea pseudogenes were found in the study. The MP tree showed that the Chinese maize (including waxy corn) has formed much independent clade. But the possible ancestors werer not in the same clad. It was indicated that the waxy corn has special origin and evolution path.2. Twenty glb1 sequences including 11 waxy corn landraces, 6 special types of cultivated maize and 3 relatives were sequenced. With 23 sequences downloaded from GENBANK 20 sequences were analyzed .The results showed that the nucleotide polymorphism of waxy corn was the most one among all taxa. The fixed differences and shared polymorphisms between all taxa sampled displayed that the waxy corn, Z.mays.ssp.parviglumis have less divergent time than and are more relative to normal maize (especially the America cultivated maize and Chinese normal maize). The waxy corn has obvious divergence to Zperennis, Z.diploperennis and Z. luxurians but is less relative to them than Z.mays.ssp.parviglumis, Z.mays.ssp.mexicana and cultivated maize. It was likely that the relationships between the waxy corn, Zmays.ssp.parviglumis and the normal cultivated maize are much close. But the possibility that the waxy corn wass mutated by the normal maize through single gene mutation was much little. It can be concluded that Zmays.ssp.parviglumis is possibly the ancestor of the cultivated corn and the waxy corn or Z.mays.ssp.parviglumis has the same ancestor with the waxy corn.3. The partial sequences of waxy gene of 23 materials including the waxy corn and the normal corn were sequenced. 40 sequences were downloaded from Genbank. Sequences
comparison, Tajiama'D test, Fu and Li's D* and Fu and Li's F* all indicated that the locus evolution of the waxy corn and the others is different, the waxy locus was effected by selection directly and its nucleotide polymorphisms decreased obviously which was related to the traditional eating habit of dwellers in the southwestern China. This is the first proved locus of the maize controlling the starth parthway which is related to artificial selection directly.4. The analysis of rpL16 sequence, ITS region and waxy gene all indicated that the genetic differentiation between coxi and waxy corn are so big that the waxy corn has no possibility of being origined from coix.5. According to phylogeography, the partial sequences of waxy gene of 77 materials including 43 waxy corn landraces and 34 non-waxy corn landraces were compared. Ten haplotypes were found in the 77 sampled sequences from different regions. Using most parsimony method and taking coix as outgroup we constructed the rooted haplotype tree. The geographical origin of the waxy corn is determined according to the topology of the MP tree, variation patterns of haplotypes and the geographical distribution of the originality haplotype. The results indicated that the waxy corn was originated from the southwest of china, exactly in partial special ecological area of the common boundary of Yunnan、 Guangxi and Guizhou, which locates between 23 ° N~25° N, nearby 105° E.6. The 2nd intron of nad1 of the mitochondrion genome and the rpL16 of the chloroplast genome were sequenced. The systematic value of the two cytoplasmic DNA sequences in maize genes evolution was clarified. It is considered that The 2nd intron of nadl change faster than rpL16 and contain more systematical information for the recostruction of Zea genus.
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