利用ILP分子标记分析籼粳杂交水稻的遗传多样性

采用ILP标记分析了福建地区20个亲本和30个育成品系构建的水稻籼粳亚种间杂交育种系谱的遗传多样性,并对结果进行聚类分析。结果表明,ILP标记可明显区分供试材料的籼粳特征。基于ILP标记聚类结果,以相似系数0.67为阈值,将该育种系谱划分成3个类群,即籼稻型、中间型和粳稻型。     

籼-粳稻特异插入／缺失分子标记揭示的稻属植物遗传分化

籼-粳分化在亚洲栽培稻(Oryza sativa L.)的驯化过程中非常重要,但其分化机制仍不清楚.有的学者认为水稻籼-粳分化是亚洲栽培稻在驯化过程中适应不同生境的结果,也有人认为籼-粳分化在水稻的野生祖先种中就已经存在.为了研究普通野生稻的籼-粳分化,并解析稻属(Oryza)植物的籼-粳遗传变异,利用34对籼-粳特异插入/缺失分子标记(InDel)引物,研究了50份典型籼稻(O.sativa L.subsp.Indica Kato)和粳稻(O.sativa L.subsp.japonica Kato)样本以及来源于35个国家的348份稻属其他种材料.结果表明,亚洲栽培稻存在明显的籼-粳分化,普通野生稻复合体(O.rufipogon complex)中存在"偏籼"和"偏粳"类型,而稻属的其他种均未出现籼-粳分化,普通野生稻复合体中"偏籼"和"偏粳"类型的地理分布格局与籼稻和粳稻的地理分布格局相吻合.考虑到大部分普通野生稻复合体的样本取自邻近有栽培稻种植的普通野生稻群体,推测得出部分普通野生稻样本中表现出的"偏籼"和"偏粳"类型可能是栽培稻的籼稻品种和粳稻品种在普通野生稻的长期协同进化过程中基因交流的结果.     

超高产杂交粳稻的遗传特征的初步分析

2012年江苏省杂交晚粳区试11份材料的平均亩产为683.24kg,仅甬优杂交组合E240(Z06)在6个试点的平均亩产达到796.1kg的超高产水平,较对照甬优8号增产15.13%.为探索该杂交组合的超高产遗传结构,利用在籼粳有多态性的分布于12条染色体的36对InDel标记检测,发现该组合的籼型基因频率为0.47,属于中间型,其他组合的籼型基因频率都低于0.4,属于粳型或偏粳型.分子标记检测杂交组合Z06在第5和第12染色体的基因型为纯合籼型和杂合型,与其他组合明显不同.广亲和基因的功能标记检测仅发现Z03、Z05和Z06这3个杂交粳稻携带广亲和基因S5n,其中Z05为纯合基因型,Z03和Z06为杂合基因型.该研究表明杂交粳稻超高产组合应该接近一半籼型一半粳型,第5和12染色体片段为籼型基因型,并携带广亲和基因.     

籼稻和粳稻的高效分子鉴定方法及其在水稻育种和进化研究中的意义

为了建立准确高效的籼稻和粳稻鉴定方法,对基于籼稻(93-11)和粳稻(日本晴)的全基因组DNA序列比对而获得的45个特异插入/缺失(InDcl)位点进行了实验验证.以包括93-11和日本睛在内的44个典型籼稻和典型粳稻品种为实验群体,用45对InDel引物对上述水稻品种的DNA样品进行了PCR扩增和聚丙烯酰胺凝胶电泳,获得了多态的电泳条带.对获得的各InDel位点的基因型数据矩阵进行了中性检测(neutrality test),确定了与栽培稻的籼、粳遗传分化密切相关的34个InDel位点.进一步对来自亚洲11个国家的栽培稻品种和来源不同12个野生稻物种的PCR产物和电泳结果的读取和分析,计算这些栽培稻品种和野生稻DNA样品在这34个InDel位点上的籼型或粳型基因频率,最终确定了不同样品的籼、粳特性.该籼稻和粳稻鉴定方法被称为"InDel分子指数法".与传统基于形态特征鉴定栽培稻籼、粳特性的"程氏指数法"相比,该方法不仅能够准确鉴定籼稻和粳稻,而且还具有更快捷、简便和高效的特点.另外,InDel分子指数法还可以用于野生稻样品的籼、粳特性鉴定,扩大了被检测样品的范围,具有广阔的应用前景.InDel分子指数法的建立为栽培稻育种过程中正确选用籼稻或粳稻种质资源提供了新的技术方法,也为栽培稻的起源、籼-粳遗传分化、以及籼稻和粳稻在驯化过程中如何适应地理环境变化提供了新的研究思路.     

籼稻和粳稻的高效分子鉴定方法及其在水稻育种和进化研究中的意义

为了建立准确高效的籼稻和粳稻鉴定方法,对基于籼稻（93—11）和粳稻（日本睛）的全基因组DNA序列比对而获得的45个特异插入／缺失（InDel）位点进行了实验验证．以包括93—11和日本晴在内的44个典型籼稻和典型粳稻品种为实验群体,用45对InDel引物对上述水稻品种的DNA样品进行了PCR扩增和聚丙烯酰胺凝胶电泳,获得了多态的电泳条带．对获得的各InDel位点的基因型数据矩阵进行了中性检测（neutrality test）,确定了与栽培稻的籼、粳遗传分化密切相关的34个InDel位点．进一步对来自亚洲11个国家的栽培稻品种和来源不同12个野生稻物种的PCR产物和电泳结果的读取和分析,计算这些栽培稻品种和野生稻DNA样品在这34个InDel位点上的籼型或粳型基因频率,最终确定了不同样品的籼、粳特性．该籼稻和粳稻鉴定方法被称为“InDel分子指数法99与传统基于形态特征鉴定栽培稻籼、粳特性的“程氏指数法”相比,该方法不仅能够准确鉴定籼稻和粳稻,而且还具有更快捷、简便和高效的特点．另外,InDel分子指数法还可以用于野生稻样品的籼、粳特性鉴定,扩大了被检测样品的范围,具有广阔的应用前景．InDel分子指数法的建立为栽培稻育种过程中正确选用籼稻或粳稻种质资源提供了新的技术方法,也为栽培稻的起源、籼-粳遗传分化、以及籼稻和粳稻在驯化过程中如何适应地理环境变化提供了新的研究思路．     

籼稻93-11和粳稻日本晴DNA插入缺失差异片段揭示的水稻籼-粳分化

碱基的插入/缺失(InDel)引起DNA序列变化并形成了DNA片段长度多态,可以用作遗传标记.为了评价基于籼稻93-11和粳稻日本晴全基因组序列比对获得的差异片段而设计的InDel引物在鉴定籼稻和粳稻两种生态型以及研究稻属不同物种之间亲缘关系的意义,采用45对InDel引物,对来自亚洲10个国家的49份籼稻、43份粳稻品种和24份野生稻进行了检验.结果表明,其中41对InDel引物鉴定籼稻或粳稻品种的准确率高于80%.主成分分析散点图显示:籼稻与粳稻存在明显的遗传分化;含AA基因组的野生稻物种与籼稻品种存在较近的亲缘关系;非AA基因组的野生稻物种不存在明显的籼-粳分化.并且证明了基于籼稻93-11和粳稻日本晴全基因组序列比对获得的InDel差异片段设计的引物可以用于栽培稻籼稻和粳稻品种的鉴定以及籼-粳分化问题的研究,及探索稻属不同物种间的亲缘关系.     

水稻遗传多样性及其农艺性状与SSR标记的关联分析

分析水稻材料的遗传多样性,寻找与农艺性状相关联的分子标记,为水稻杂交组合的配置及分子标记辅助育种提供依据.利用60对分布于水稻12条染色体组的SSR标记对190份水稻材料进行遗传多样性分析与群体遗传结构分析,并采用Tassel3.0的GLM和MLM进行标记与农艺性状的关联分析.结果显示,190份水稻材料的遗传相似系数(GS)变异范围为0.62～0.97,平均值为0.86.按群体遗传结构可将供试材料分为3个亚群.以GLM分析,发现8个与穗长、一次枝梗数、一次枝梗穗粒数、二次枝梗数、二次枝梗穗粒数、总穗粒数和饱满穗粒数相关联的标记,各标记对表型变异的解释率为0.0648;以MLM分析显示,8个标记对表型变异的解释率在0.0378～0.0648.本研究获得的这8个农艺性状相关的分子标记可以作为辅助育种培育高产水稻品种的分子标记.     

亚洲栽培稻5种不同生态类型与籼粳间的杂种F1育性研究

为全面系统地研究亚洲栽培稻种内不同生态类型材料与籼、粳亚种杂交育性，对19份包含亚洲栽培稻种内5种不同生态类型品种与云南温带粳品种滇粳优1号及国际水稻所选育的籼稻品种IR64的杂种F₁育性进行分析.结果表明，亚洲栽培稻不同类型中，温带粳与籼亚种间普遍存在杂种不育，温带粳与热带粳间、籼籼部分组合也存在杂种不育，Aus类型与籼、粳亚种的杂种不育程度与品种相关.研究结果为系统研究亚洲栽培稻不同生态类型与籼、粳间杂种不育奠定了基础，为认识亚洲栽培稻的分化提供证据，并为利用亚洲栽培稻种内丰富的遗传变异来培育新品种、新组合提供理论指导.     

花粉愈伤组织群体偏态分离的SSR标记鉴定

利用水稻花粉育性基因S-b的SSR分子标记RMl3，鉴定籼粳稻杂种Fl的花粉愈伤组织的基因型，以确定每块愈伤组织在S-b座位的遗传来源，结果表明该座位的等位基因S^i或S^j在愈伤组织群体中分离比不符合1：1的规律，出现偏态分离现象．选择不同培养基及增加预冷处理不会改变偏态分离的方向，但预冷处理会增大偏分离的趋势．为进一步解释DH群体构建中的某些基因的偏态分离现象提供了依据，同时讨论了将SSR标记引入组织培养体系的可行性．     

微卫星标记分析籼粳亚种间的遗传多样性

208对引物中具有多态性的引物123对，占所用引物的59．13％，不同染色体的微卫星分析的多态性不同，染色体9，10微卫星的多态性高于其它染色体，染色体12上的微卫星标记的多态性最差，仅为46．15％．聚类分析表明，所有的供试材料可分为两群，即籼稻群和粳稻群，聚类结果与亲本材料亲缘关系基本一致，说明微卫星标记能较好地区分籼稻和粳稻，由于农艺性状是基因表达的结果，易受环境影响，聚类结果不能从整体上充分反应品种间的遗传变异，42份常用杂交水稻亲本材料聚类分析表明，恢复系和不育系遗传基础均较狭窄，但恢复系和不育系之间的遗传距离相对较远，从一定程度上反映了遗传距离与杂种优势正相关。     

Experimental validation of inter-subspecific genetic diversity in rice represented by the differences between the DNA sequences of ‘Nipponbare’ and ‘93-11’

The pedigrees of three sequenced rice cultivars were analyzed to show that a majority of the genetic composition of 'Nipponbare' originates from japonica cultivars while the minority originates from indica cultivars. In contrast, '93-11' is derived mainly from indica cultivars with a smaller contribution from japonica cultivars. All ancestors of 'Guang lu ai 4' appeared to be indica lines. A set of molecular markers (46 InDels and 53 SSRs) polymorphic between 'Nipponbare' and '93-11' were examined in 46 typical indica and 47 typical japonica cultivars selected from 443 accessions according to Cheng's index. All cultivars were divided into indica and japonica groups without overlapping when clustered by Cheng's index, InDels and SSRs. Much higher InDel and SSR diversity between groups than within groups implies that the marker polymorphisms between 'Nipponbare' and '93-11' represent a large proportion of inter-subspecific diversity. About 85% of indica cultivars and more than 90% of japonica cultivars were confirmed to have the same PCR banding patterns as '93-11' and 'Nipponbare', respectively. Some polymorphic loci between 'Nipponbare' and '93-11' cannot be validated in other indica and japonica cultivars, either as subspecies-specific but not predominant alleles, or alleles not specific between the two groups. It was concluded that molecular markers developed from sequence polymorphism between 'Nipponbare' and '93-11' often represent inter-subspecific diversity, although some exceptions were sensitive to either particular marker loci or particular cultivars.     

Efficient indica and japonica rice identification based on the InDel molecular method: Its implication in rice breeding and evolutionary research

An efficient molecular method for the accurate and efficient identification of indica and japonica rice was created based on the poly-morphisms of insertion/deletion (InDel) DNA fragments obtained from the basic local alignment search tool (BLAST) to the entire genomic sequences of indica (93-11) and japonica rice (Nipponbare). The 45 InDel loci were validated experimentally by the polymerase chain reaction (PCR) and polyacrylamide gel electrophoresis (PAGE) in 44 typical indica and japonica rice varieties, including 93-11 and Nipponbare. A neutrality test of the data matrix generated from electrophoretic banding patterns of various InDel loci indicated that 34 InDel loci were strongly associated with the differentiation of indica and japonica rice. More extensive analyses involving cultivated rice varieties from 11 Asian countries, and 12 wild Oryza species with various origins confirmed that indica and japonica characteristics could accurately be determined via calculating the average frequency of indica- or japonica-specific alleles on different InDel loci across the rice genome. This method was named as the "InDel molecular index" that combines molecular and statistical methods in determining the indica and japonica characteristics of rice varieties. Compared with the traditional methods based essentially on morphology, the InDel molecular index provides a very accurate, rapid, simple, and efficient method for identifying indica and japonica rice. In addition, the InDel index can be used to determine indica or japonica characteristics of wild Oryza species, which largely extends the utility of this method. The InDel molecular index provides a new tool for the effective selection of appropriate indica or japonica rice germplasm in rice breeding. It also offers a novel model for the study of the origin, evolution, and genetic differentiation of indica and japonica rice adapted to various environmental changes.     

Spacer length variation in rice 5S rRNA genes revealed by polymerase chain reaction

Polymerase chain reaction (PCR) was used to amplify 5S rRNA spacer from wild rice (Oryza rufipogon and O. nivara) and cultivated rice (indica and japonica varieties of O. sativa L). The results show that there is spacer length variation within and between species, and the typical indica and japonica varieties have their unique banding patterns of amplified 5S rRNA spacers, whereas intermediate showed no specific amplification profile of spacer regions. The 5S rRNA genes in intermediate are either identical with that of indica variety or that of japonica variety. These data suggest that the spacer length polymorphisms can be used to distinguish between closely ralated species and subspecies. Supported by the National Natural Science Foundation of China Yi Qingming, born in Apr. 1938, Professor     

SSR标记对籼稻品种的遗传多样性分析

利用500多对SSR标记对广陆矮4号、珍汕97B、佳辐占、明恢86和明恢63 5个籼稻亲本品种进行遗传多样性分析.结果表明,佳辐占与明恢63、明恢86、珍汕97B和广陆矮4号之间的相似系数分别为78.1%、76.1%、72.8%和71.7%.相对而言,其相似系数越小,遗传距离越大,因此利用佳辐占与这些品种组配较有希望选育出品质优良、综合优势明显的新品系.同时研究表明,标记间平均距离为10 cM或小于10 cM时,分析所得结果较为可靠.     

Characteristics of the short rachillae of rice from archaeological sites dating to 7000 years ago

The abscission layer formed on a pedicel situated at the basal part of a short rachilla is an important characteristic for discriminating between wild, japonica, and indica rice. The short rachillae of paddy rice grains excavated from the Kuahuqiao, Luojiajiao, and Tianluoshan sites, located in the lower reaches of the Yangtze River and dating to 7000 years old, were observed. The results showed that the short rachillae could be divided into two types: a wild type and japonica type. These results indicated that the rice had been domesticated, but was a primitive cultivated rice that retained some of the characteristics of wild rice. The results also suggested that the rice was changing to resemble japonica type rice. Based on the ratios of wild and japonica types, it was inferred that rice domestication began 10000 years ago.     

短日照对几种不同光反应型水稻生长发育的影响

以自然日照为对照,在塑料大棚内对比观察了4个不同光反应型水稻品种在生长发育的各阶段对短日照的反应特性。结果表明：早粳晚熟品种、中粳中熟品种在3～4叶龄短日照处理20～30d开始对短日照有反应,主茎叶龄6～7叶时植株对日照长度最敏感,抽穗时间(由播种期到抽穗期的时间)较对照减少约26天;晚熟品种对日照长度反应的时期晚。不同品种的主茎叶片数、株高与抽穗时间成正相关,且达极显著水平,但籼稻品种的相关系数最小。短日照对早粳晚熟品种辽5和中粳中熟品种冀粳8号的穗粒数和结实率的影响很大：在7叶龄5～10d的短日照处理条件下,辽5的穗粒数和结实率与对照相差最小;冀粳8号最适宜的短日处理分别为7叶龄10h短日照处理5～10d,中粳晚熟品种冀糯1号在7叶龄15d的短日照处理条件下,短日照对其穗粒数和结实率的影响最小;6叶龄20d短日照处理对籼稻品种南农大的穗粒数和结实率的影响最小。     

利用粳稻基因组DNA和C_ot-1 DNA探针对普通野生稻和亚洲栽培稻的比较分析

以粳稻日本晴基因组DNA和Cot-1 DNA为探针,分别对日本晴、籼稻广陆矮4号和普通野生稻的染色体组进行了基因组原位杂交(GISH)和Cot-1 DNA荧光原位杂交(FISH)分析,并对3种染色体组进行了同源聚类和比较研究.结果表明:粳稻基因组DNA和Cot-1 DNA探针信号在3种水稻染色体组中的分布状况和覆盖率相似,Cot-1 DNA的覆盖率分别为(47.13±0.18)%、(45.89±0.22)%、(44.24±0.21)%,3种水稻基因组同源性高,亲缘关系接近.Cot-1 DNA在3种水稻染色体上的杂交信号分布各有特点,中高度重复序列的变异在普通野生稻向栽培稻进化和亚洲栽培稻籼、粳分化过程中具有重要意义,中高度重复序列含量较低的2、5、8号染色体是水稻染色体组进化过程中相对活跃的成分.