穞稻与栽培稻杂种花粉不育性的细胞学研究及基因定位
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摘要
穞稻是我国长江下游地区具有杂草习性的独特的稻种资源，主要分布在江苏省连云港地区(34°33′-34°46′N，119°13′-119°30′E)。由于其特殊的地理分布，以及对研究中国栽培稻起源分化的潜在价值，穞稻自从十九世纪六十年代被发现以来已引起人们较多的关注，但它在稻属中的分类地位目前仍存在争论。此外，由于穞稻与现代栽培稻之间存在着广泛的生殖障碍，严重限制了其特有的耐盐耐旱等众多优良性状在水稻育种实践中的应用。本研究结合杂交亲和性和SSR(simple sequence repeats)标记分析，对穞稻与现代栽培稻之间的亲缘关系进行了探讨；并重点对穞稻与典型粳稻品种秋光的杂种花粉不育性进行了细胞学机理和基因定位等方面的研究。主要研究结果如下：
1．穞稻与现代栽培稻亲缘关系的探讨
通过分析穞稻与籼型测验种、粳型测验种以及广亲和品种杂种的小穗和花粉育性，发现穞稻与粳型栽培品种的亲和性较好，而与籼型栽培品种的亲和性较差。进一步利用SSR标记对穞稻和21个栽培品种之间的遗传相似性进行研究，并根据遗传距离对它们进行聚类分析。结果发现穞稻与所有粳型品种聚为一类，但是它与粳型品种之间的遗传距离不及粳型品种相互之间的遗传距离近。
2．穞稻与秋光杂种花粉不育的细胞学机理
穞稻/秋光杂种F_1的花粉表现为半不育，且正反交两组合的花粉育性差异不显著。在穞稻/秋光杂种中，小孢子发生和单核花粉形成的过程与亲本品种秋光没有明显差异。但是，穞稻/秋光杂种花粉在从晚期小孢子到成熟花粉的转变过程中发生了明显异常。异常现象主要包括两种：其中之一是在从单核向二核发育的过程中，一些小孢子的形状发生异常；另外一种情况是在晚期二核花粉时期，很大一部分花粉的生殖核和营养核相继解体，在花粉的中央形成巨大的染色质团块，最终导致花粉败育。在穞稻/秋光杂种的整个花粉发育过程中，绒毡层和其它花药壁的形成和降解均没有发生异常现象。
3．水稻分子连锁图谱的构建及标记偏分离分析
利用包含215个单株的秋光//穞稻/秋光BC_1F_1群体构建了一张分子连锁图谱，其全长为1597.0cM，包含118个SSR标记和1个EST(expressed sequence tag)标记，平均图距为13.4cM。在该图谱中，共有30个标记位点检测到偏分离的发生，分别位于第2、3、4、6、8、9、10和11染色体上。其中，最为严重的偏分离发生在第3染色体上一个很长的染色体区段内。
4．杂种花粉不育QTL的检测与分析
根据构建的分子连锁图谱，在第3和11染色体上检测到2个控制杂种花粉不育性的QTL，qPS-3和qPS-11。其中，qPS-3与EST标记C0729连锁，LOD值为52.6，贡献率为57.9％；qPS-11与SSR标记RM552连锁，LOD值为32.1，贡献率为32.5％。这两个位点可能均为新的杂种花粉不育基因，暂时分别命名为S33(t)和S34(t)。这2个基因之间不存在明显的互作效应，彼此独立控制花粉育性，但对花粉育性的影响具有累加效应，其中S33(t)比S34(t)的效应更强一些。杂种花粉育性的下降是由于各位点内等位基因的互作引起的，广亲和品种02428在S33(t)和S34(t)两位点分别携有中性等位基因。
5．水稻杂种花粉不育新基因S33(t)的精细定位
为了精细定位主效基因，S33(t)，我们从秋光//穞稻/秋光BC_1F_1群体中选择花粉育性在80％以上的单株，并用新开发的SSR和InDel(insertion/deletion)标记分析这些单株的重组行为。结果把S33(t)定位到SSR标记RM15621和RM15627之间86kb的染色体区段；序列分析表明，该区域内存在10个开放阅读框。此研究结果为该基因的图位克隆以及在水稻育种中通过分子标记辅助选择来转移相关中性等位基因奠定了一定的基础。
Ludao, a weedy rice strain in lower Yangtze valley, grows naturally in the fields of Lianyungang region (34°33'-34°46'N, 119o13'-119°30'E), east China's Jiangsu province (Jiang et al, 1985). Due to its sepecific geographic distribution and the potential significance on the understanding of the origin and differentiation of Chinese rice cultivars, Ludao has been attached increasing attention since it was discovered in 1960's. However, so far no consensus on its taxonomic status has been reached. Moreover, the ubiquitous reproductive barriers between Ludao and modern cultivar of rice have restrained extremely its application of excellent characters such as high salinity and drought tolerance in rice breeding. In our study, combined with crossing affinity and SSR assay, approach to clarify the relationship between Ludao and modern cultivated varieties was conducted, with emphasis on cytological mechanism and gene mapping of pollen sterility in hybrids between Ludao and a typical japonica variety, Akihikari. The results are as follows:
1. The relationship between Ludao and modern cultivated varieties
The spikelet and pollen fertility of hybrids between Ludao and tested cultivar, indica, japonica as well as wide compatibility varieties showed that crossing affinity of Ludao with japonica varieties was closer compared with indica varieties. SSR assay was used to further investigate the genetic similarity between Ludao and 21 cultivated varieties, and cluster analysis was undertaken based on the genetic distance between them. The results proved that Ludao and japonica varieties were grouped into one type, but the genetic distance of which was greater than that between japonica varieties.
2. Cytological mechanism of pollen abortion in the Ludao/Akihikari hybrid
Hybrids pollen of Ludao/Akihikari showed partial pollen sterility, same to the F_1 pollen of reciprocal. During the process of microsporogenesis and uni-nucleate pollen formation, the pollen development of Ludao/Akihikari hybrid is indistinguishable from it's parent, Akihikari. Visible differences of pollens between Ludao/Akihikari hybrid and Akihikari began at the transition from late microspores to mature pollens. Two types of abnormalities were observed in hybrid pollens. In the first type, at the stage of a single nucleus to two nuclei of microspore development, some microspores became abortive as indicated by their irregular shape. In the second type, during the late bicellular pollen stage, a large proportion of pollen generative and vegetative cells began to disaggregate gradually, and shape a bigger chromatin conglomeration across pollen center, eventually leading to abortion of the pollens. No visible abnormality in the development and disintegration of tapetum and other anther walls during microspore formation and development in the Ludao/Akihikari hybrid.
3. Construction of molecular linkage map and analysis of distorted segregation
A molecular linkage map consisted of 118 SSR markers and 1 EST marker was constructed using 215 individual plants of Akihikari//Ludao/Akihikari, with a total length of 1597.0cM on all 12 chromosomes with an average interval of 13.4cM. Segregation distortions of markers totaled 30 distributed on chromosome 2, 3, 4, 6, 8, 9, 10 and 11, respectively. Among which, the most pronounced one lies in a wide region on chromosome 3.
4. Detection and analysis of QTL for hybrid pollen sterility
In virtue of the constructed molecular linkage map, two putative QTLs controlling hybrid pollen sterility were detected on chromosomes 3 and 11, and designated as qPS-3 and qPS-11 respectively.The former was linked with the EST marker C0729 with LOD score of 52.6 and PVE (phenotypic variance explained) of 57.9% and the later, with LOD score of 32.1 was linked with the SSR marker RM552 accounted for 32.5% of PVE. Both loci are different from those reported previously and then designated as S33(t) and S34(t) respectively. No interaction was detected between the two loci, which affected pollen sterility independently with additive effects, with S33(t) more effect on pollen sterility than S34(t). Interaction between the Ludao and Akihikari alleles at each of the two loci resulted in a reduction in pollen fertility, and wide compatible variety 02428 was considered to possess the neutral allele at loci S33(t) and S34(t) respectively.
5. Fine mapping of novel gene S33(t) for hybrid pollen sterility
To determine the precise map location of S33(t), a major locus for hybrid pollen sterility, individual plants with pollen fertility higher than 80.0% from BC_1F_1 population of Akihikari//Ludao/Akihikari were selected and recombination events surrounding the S33(t) locus were assayed using SSR and InDel markers newly developed. As a result, S33(t) was delimited to an 86 kb region between SSR markers RM15621 and RM15627. Sequence analysis of which revealed that ten ORFs (open reading frame) were included. These results will be valuable for cloning the corresponding gene and for marker-assisted transferring of the related neutral allele in rice breeding programs.
1．穞稻与现代栽培稻亲缘关系的探讨
通过分析穞稻与籼型测验种、粳型测验种以及广亲和品种杂种的小穗和花粉育性，发现穞稻与粳型栽培品种的亲和性较好，而与籼型栽培品种的亲和性较差。进一步利用SSR标记对穞稻和21个栽培品种之间的遗传相似性进行研究，并根据遗传距离对它们进行聚类分析。结果发现穞稻与所有粳型品种聚为一类，但是它与粳型品种之间的遗传距离不及粳型品种相互之间的遗传距离近。
2．穞稻与秋光杂种花粉不育的细胞学机理
穞稻/秋光杂种F_1的花粉表现为半不育，且正反交两组合的花粉育性差异不显著。在穞稻/秋光杂种中，小孢子发生和单核花粉形成的过程与亲本品种秋光没有明显差异。但是，穞稻/秋光杂种花粉在从晚期小孢子到成熟花粉的转变过程中发生了明显异常。异常现象主要包括两种：其中之一是在从单核向二核发育的过程中，一些小孢子的形状发生异常；另外一种情况是在晚期二核花粉时期，很大一部分花粉的生殖核和营养核相继解体，在花粉的中央形成巨大的染色质团块，最终导致花粉败育。在穞稻/秋光杂种的整个花粉发育过程中，绒毡层和其它花药壁的形成和降解均没有发生异常现象。
3．水稻分子连锁图谱的构建及标记偏分离分析
利用包含215个单株的秋光//穞稻/秋光BC_1F_1群体构建了一张分子连锁图谱，其全长为1597.0cM，包含118个SSR标记和1个EST(expressed sequence tag)标记，平均图距为13.4cM。在该图谱中，共有30个标记位点检测到偏分离的发生，分别位于第2、3、4、6、8、9、10和11染色体上。其中，最为严重的偏分离发生在第3染色体上一个很长的染色体区段内。
4．杂种花粉不育QTL的检测与分析
根据构建的分子连锁图谱，在第3和11染色体上检测到2个控制杂种花粉不育性的QTL，qPS-3和qPS-11。其中，qPS-3与EST标记C0729连锁，LOD值为52.6，贡献率为57.9％；qPS-11与SSR标记RM552连锁，LOD值为32.1，贡献率为32.5％。这两个位点可能均为新的杂种花粉不育基因，暂时分别命名为S33(t)和S34(t)。这2个基因之间不存在明显的互作效应，彼此独立控制花粉育性，但对花粉育性的影响具有累加效应，其中S33(t)比S34(t)的效应更强一些。杂种花粉育性的下降是由于各位点内等位基因的互作引起的，广亲和品种02428在S33(t)和S34(t)两位点分别携有中性等位基因。
5．水稻杂种花粉不育新基因S33(t)的精细定位
为了精细定位主效基因，S33(t)，我们从秋光//穞稻/秋光BC_1F_1群体中选择花粉育性在80％以上的单株，并用新开发的SSR和InDel(insertion/deletion)标记分析这些单株的重组行为。结果把S33(t)定位到SSR标记RM15621和RM15627之间86kb的染色体区段；序列分析表明，该区域内存在10个开放阅读框。此研究结果为该基因的图位克隆以及在水稻育种中通过分子标记辅助选择来转移相关中性等位基因奠定了一定的基础。
Ludao, a weedy rice strain in lower Yangtze valley, grows naturally in the fields of Lianyungang region (34°33'-34°46'N, 119o13'-119°30'E), east China's Jiangsu province (Jiang et al, 1985). Due to its sepecific geographic distribution and the potential significance on the understanding of the origin and differentiation of Chinese rice cultivars, Ludao has been attached increasing attention since it was discovered in 1960's. However, so far no consensus on its taxonomic status has been reached. Moreover, the ubiquitous reproductive barriers between Ludao and modern cultivar of rice have restrained extremely its application of excellent characters such as high salinity and drought tolerance in rice breeding. In our study, combined with crossing affinity and SSR assay, approach to clarify the relationship between Ludao and modern cultivated varieties was conducted, with emphasis on cytological mechanism and gene mapping of pollen sterility in hybrids between Ludao and a typical japonica variety, Akihikari. The results are as follows:
1. The relationship between Ludao and modern cultivated varieties
The spikelet and pollen fertility of hybrids between Ludao and tested cultivar, indica, japonica as well as wide compatibility varieties showed that crossing affinity of Ludao with japonica varieties was closer compared with indica varieties. SSR assay was used to further investigate the genetic similarity between Ludao and 21 cultivated varieties, and cluster analysis was undertaken based on the genetic distance between them. The results proved that Ludao and japonica varieties were grouped into one type, but the genetic distance of which was greater than that between japonica varieties.
2. Cytological mechanism of pollen abortion in the Ludao/Akihikari hybrid
Hybrids pollen of Ludao/Akihikari showed partial pollen sterility, same to the F_1 pollen of reciprocal. During the process of microsporogenesis and uni-nucleate pollen formation, the pollen development of Ludao/Akihikari hybrid is indistinguishable from it's parent, Akihikari. Visible differences of pollens between Ludao/Akihikari hybrid and Akihikari began at the transition from late microspores to mature pollens. Two types of abnormalities were observed in hybrid pollens. In the first type, at the stage of a single nucleus to two nuclei of microspore development, some microspores became abortive as indicated by their irregular shape. In the second type, during the late bicellular pollen stage, a large proportion of pollen generative and vegetative cells began to disaggregate gradually, and shape a bigger chromatin conglomeration across pollen center, eventually leading to abortion of the pollens. No visible abnormality in the development and disintegration of tapetum and other anther walls during microspore formation and development in the Ludao/Akihikari hybrid.
3. Construction of molecular linkage map and analysis of distorted segregation
A molecular linkage map consisted of 118 SSR markers and 1 EST marker was constructed using 215 individual plants of Akihikari//Ludao/Akihikari, with a total length of 1597.0cM on all 12 chromosomes with an average interval of 13.4cM. Segregation distortions of markers totaled 30 distributed on chromosome 2, 3, 4, 6, 8, 9, 10 and 11, respectively. Among which, the most pronounced one lies in a wide region on chromosome 3.
4. Detection and analysis of QTL for hybrid pollen sterility
In virtue of the constructed molecular linkage map, two putative QTLs controlling hybrid pollen sterility were detected on chromosomes 3 and 11, and designated as qPS-3 and qPS-11 respectively.The former was linked with the EST marker C0729 with LOD score of 52.6 and PVE (phenotypic variance explained) of 57.9% and the later, with LOD score of 32.1 was linked with the SSR marker RM552 accounted for 32.5% of PVE. Both loci are different from those reported previously and then designated as S33(t) and S34(t) respectively. No interaction was detected between the two loci, which affected pollen sterility independently with additive effects, with S33(t) more effect on pollen sterility than S34(t). Interaction between the Ludao and Akihikari alleles at each of the two loci resulted in a reduction in pollen fertility, and wide compatible variety 02428 was considered to possess the neutral allele at loci S33(t) and S34(t) respectively.
5. Fine mapping of novel gene S33(t) for hybrid pollen sterility
To determine the precise map location of S33(t), a major locus for hybrid pollen sterility, individual plants with pollen fertility higher than 80.0% from BC_1F_1 population of Akihikari//Ludao/Akihikari were selected and recombination events surrounding the S33(t) locus were assayed using SSR and InDel markers newly developed. As a result, S33(t) was delimited to an 86 kb region between SSR markers RM15621 and RM15627. Sequence analysis of which revealed that ten ORFs (open reading frame) were included. These results will be valuable for cloning the corresponding gene and for marker-assisted transferring of the related neutral allele in rice breeding programs.
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