Genetic analysis of morphological index and its related taxonomic traits for classification of indica/japonica rice

A doubled haploid population derived from anther culture of ZYQ8/JX17 F₁, a typical indica and japonica hybrid, was used in this study. Morphological index and its related taxonomic traits were investigated in 121 DH lines. The quantitative trait loci (QTLs) for morphological index and its related taxonomic traits were analyzed. Two major QTLs for leaf hairiness, three QTLs for length/width of grain, one QTL for color of hull when heading, one QTL for hairiness of hull, two QTLs for length of the first and second panicle internode, and one major QTL and two QTLs for phenol reaction were detected. Four QTLs for morphological index were also identified on chromosomes 1, 3, 4 and 6, respectively, three of which on chromosomes 1, 3 and 6, respectively, were found to be located in the same chromosome regions where some QTLs for the related taxonomic traits were located.     

典型籼粳杂种不育性的分子标记分析及其遗传基础

对典型籼粳杂种育性遗传基础的研究是快速进行广亲和系培育的前提。以回交群体Balilla/南特号∥Balilla为育性基因的分析群体,利用SSR标记研究了该群体中控制小穗育性和花粉育性的基因位点,对于小穗育性共检测到2个QTLs,Qsptf1和qSPTF6,分别位于第1和第6染色体上,其加性效应分别为13．501和—16．414。根据前人的研究结果,以及qSPTF6在第6染色体上所处的位置,可以推断qSPTF6即为S—5位点。在花粉育性的QTLs检测中,发现在第7和第9染色体上有两个QTLs,qPLLN7和qPLLN9,其加性效应分别为—12．003和—11．012,可以分别解释表型变异的12．9％和10．3％。位点的互作分析表明,在该研究群体中,存在大量的位点互作影响小穗育性和花粉育性,在0．005显著水平上,检测到61对和51对位点互作分别影响小穗育性和花粉育性。说明籼粳杂种的不育性除了主效基因的单独作用以外,位点之间的互作,即上位性也是一重要的遗传因素。     

新疆胡颓子属植物花部性状的变异及其分类学价值

新疆胡颓子属植物栽培历史久、变异丰富、种下变异类型多、分类较为困难,因此有必要进一步发掘该属落叶组植物的分类学特征,尤其是对相对保守的繁殖器官的性状进行筛选。该研究以形态较为稳定的繁殖器官为切入点,分析花部性状的变异特点,筛选稳定性状,以期为解决该属的分类难题提供依据。先采用定株采集和同花标记的方法,对比分析了柱头形态、花盘先端有毛无毛、花柱与雄蕊的长短比、花被裂片程度四个性状的稳定性。结果表明:花盘先端有毛无毛、花柱与雄蕊的长短比、花被裂片程度三个性状较稳定,可以作为分类依据;柱头形态在单花中表现稳定,但在单株中出现极大的变异,不具有分类价值;然后采取新疆南、北疆地区的胡颓子属落叶组的尖果沙枣、大果沙枣和沙枣这三种来验证花部性状的稳定性,证明了上述结论的正确性,同时也是对该属分类研究实践的应用。该结果可为胡颓子属的经典分类学和形态学研究以及植物的开发和利用等提供参考依据。     

Weighting fibre and morphological traits in a genetic index for an alpaca breeding programme

Nowadays, the fibre diameter (FD) is considered the main selection objective in alpaca populations all over the world. International Committee for Animal Recording recommendations define the FD and its CV as the first two traits to be considered in breeding programmes for this specie. In addition to these main criteria, other selection criteria of economic value used are comfort factor (CF) or standard deviation (s.d.); also other less important traits being used as selection objectives are these morphological traits: density (DE), crimp (CR) or lock structure (LS) for, respectively, Huacaya (HU) and Suri (SU) ecotypes, head (HE), coverage (CO) and balance (BA). The goal of this study was to establish how to implement a combined selection index starting from genetic parameters and to study the expected correlation between genetic trends by considering different alternative procedures of weighting all the involved traits, and the consequences of a wrongly proceeding way. Heritabilities and genetic and phenotypic correlations were estimated from the data set belonging to the PACOMARCA experimental farm for SU and HU. Two approaches were used to check the consequences of a set of subjective weights essayed. The coefficients of selection indexes were obtained for two sets of reference weights. In addition, equivalent weights were drawn if applied those reference values as coefficients of hypothetical selection indexes directly on phenotypes; relative expected genetic responses were computed in different cases. Results showed that almost in all cases for both ecotypes, the weight applied to CF should be surprisingly negative. Concerning genetic responses, only CO was compromised in some cases for the HU ecotype. The essayed methodology allowed explaining the differences between ecotypes in the genetic trends. The proposed methodology was shown to be effective to study the relative importance of the traits granted by the manager of a breeding scheme.     

三种养殖模式下日本鳗鲡养成品的形质差异

随机选取池塘专养(M1)、日本沼虾套养(M2)以及水库放养(M3)3种养殖模式下培育的肛长为(25.91±3.26) cm的日本鳗鲡作为研究材料,比较了不同养殖模式下日本鳗鲡的形质指标,并采用聚类分析、主成分分析和判别分析等方法研究了3种养殖模式日本鳗鲡养成品的差异.结果表明:在所涉21项生物学指标和23项形质评价指数中,M1与M2之间具显著差异的分别为15项和14项,M1与M3之间具显著差异的分别为19项和18项,M2与M3之间具显著差异的分别为11项和8项;M1-M2、M1-M3、M2-M3之间的欧氏距离依次为1.433、3.516和2.167,均具显著差异;经主成分分析,提取到的5个特征值均大于1的主成分,累计贡献率达82.1％,其中第1主成分和第2主成分依次为与体型相关的肥瘦因子和与摄食行为相关的运动因子,后3个主成分为与营养状况有关的消化吸收因子,仅通过第1主成分便可较清晰地将3种养殖模式试验对象分开;采用逐步判别法,以判别贡献率较大的体宽/肛长、体长/肛长、净体积系数、鳔体积系数和肝系数为自变量,所建Fisher分类函数方程组可清晰区分3种模式的养殖群体,其判别准确率和综合判别准确率均为100％.     

Genetic and molecular dissection of quantitative traits in rice

Recent progress in the generation of a molecular genetic map and markers for rice has made possible a new phase of mapping individual genes associated with complex traits. This type of analysis is often referred to as quantitative trait locus (QTL) analysis. Increasing numbers of QTL analyses are providing enormous amounts of information about QTLs, such as the numbers of loci involved, their chromosomal locations and gene effects. Clarification of genetic bases of complex traits has a big impact not only on fundamental research on rice plant development, but it also has practical benefits for rice breeding. In this review, we summarize recent progress of QTL analysis of several complex traits in rice. A strategy for positional cloning of genes at QTLs is also discussed.     

An improved procedure for plant regeneration from indica and japonica rice protoplasts

Plant regeneration from protoplasts of two commercially cultivated Indian indica rice varieties, Pusa Basmati 1 and Java, has been accomplished by plating embryogenic cell suspension-derived protoplasts on the surface of filter membranes overlying agarose-embedded feeder cells of Lolium multltiflorum and Oryza ridleyi, combined with the use of a maltose-containing shoot regeneration medium. Embryogenic cell suspension cultures of Pusa Basmati 1 and Jaya were initiated from mature seed scutellum-derived calli in liquid R₂ medium modified by the addition of 560 mg l^–1 of proline and 1.0 % (w/v) maltose. In both varieties, protoplast plating efficiencies up to 0.4 % were obtained, depending on the nature of the feeder cells. L. multiflorum feeder cells induced a 6-fold higher plating efficiency than feeder cells of O. ridleyi. In combination, O. ridleyi and L. multiflorum feedercells further enhanced protoplast plating efficiency. Protoplast-derived cell colonies were not obtained from protoplasts of either indica varieties in the absence of feeder cells. MS-based medium containing kinetin (2.0 mg l^–1) and -naphthaleneacetic acid (0.5 mg 1^–1), together with sucrose and maltose both at 1.5 % (w/v), induced green shoot regeneration in 44 % of protoplast-derived tissues, depending on the feeder cells used for protoplast culture. In both varieties, tissues obtained using O. ridleyi feeder cells were more morphogenic than tissues obtained using L. multiflorum feeder cells, either alone or in combination with cells of O. ridleyi. In the japonica rice variety Taipei 309, this new procedure resulted in a 30-fold increase in plant regeneration from protoplasts compared to previous published procedures.Abbreviations 2,4-D 2,4-dichlorophenoxyacetic acid - FDA fluorescein diacetate - GPFs growth promoting factors - NAA -naphthaleneacetic acid On leave from Department of Genetics, Haryana Agricultural University, Hisar, IndiaOn leave from Biotechnology Centre, Punjab Agricultural University, Ludhiana, India     

粳稻穗部性状遗传分析

从粳稻（Oryzasativassp.japonica）RIL群体中选取每穗颖花数极端少的品系丙堡3201和丙堡3205及每穗颖花数极端多的品系丙堡3145和丙堡3214,配制丙堡3201×丙堡3145和丙堡3214×丙堡3205两个组合的P1、P2、F1、B1、B2和F26个世代,调查每穗颖花数、每穗实粒数、穗长、一次枝梗数和二次枝梗数的表型分布,并运用主基因＋多基因混合遗传模型,对这5个性状进行了遗传分析。结果表明,每穗颖花数性状在2个组合的各分离世代均未出现超亲分离,而其它4个性状均有不同程度的超亲分离。一次枝梗数受1对主基因＋多基因控制;其余4个性状均受2对主基因＋多基因控制。每穗颖花数、每穗实粒数、穗长和二次枝梗数4个性状以主基因遗传为主,一次枝梗数性状以多基因遗传为主。     

籼粳杂种双单倍体的配子选择

对典型的灿与粳稻杂种,窄叶青８号／京系１７Ｆ１花药进行培养获得的１３２个双单倍体的形态特性、同工酶与ＲＦＬＰ标记的分离与重组进行了考察分析,研究是否存在配子选择问题。结果表明：（１）对４个重要数量性状和６个涉及籼、粳特征的形态指数进行考察所获数据均为连续分布,并呈正态曲线;（２）用８种同工酶对５２个ＤＨ系分析结果表明,只有２种同工酶显著偏离期望的１：１比率,而灿与粳的总基因型比率相近;（３）应用１６７个ＲＦＬＰ标记对１３２个ＤＨ系进行的分析发现,有３６％标记发生偏分离,但偏籼与偏粳的比率相近,两个亲本基因组在ＤＨ群体中所占比率相同（各５０％）,各种基因组成呈正态分布。综上所述,本研究虽观察到一些轻微偏分离现象,但籼粳基因基本上随机分离与重组,等位基因总频率未偏离１：１比率。     

Quantification of total genomic DNA and selected repetitive sequences reveals concurrent changes in different DNA families in indica and japonica rice

This paper describes a fluorescence in situ hybridization (FISH) analysis of three different repetitive sequence families, which were mapped to mitotic metaphase chromosomes and extended DNA fibers (EDFs) of the two subspecies of rice (Oryza sativa), indica and japonica (2n=2x=24). The repeat families studied were (1) the tandem repeat sequence A (TrsA), a functionally non-significant repeat; (2) the [TTTAGGG]_n telomere sequence, a non-transcribed, tandemly repeated but functionally significant repeat; and (3) the 5S ribosomal RNA (5S rDNA). FISH of the TrsA repeat to metaphase chromosomes of indica and japonica cultivars revealed clear signals at the distal ends of twelve and four chromosomes, respectively. As shown in a previous report, the 17S ribosomal RNA genes (17S rDNA) are located at the nucleolus organizers (NORs) on chromosomes 9 and 10 of the indica cultivar. However, the japonica rice lacked the rDNA signals on chromosome 10. The size of the 5S rDNA repeat block, which was mapped on the chromosome 11 of both cultivars, was 1.22 times larger in the indica than in the japonica genome. The telomeric repeat arrays at the distal ends of all chromosome arms were on average three times longer in the indica genome than in the japonica genome. Flow cytometric measurements revealed that the nuclear DNA content of indica rice is 9.7% higher than that of japonica rice. Our data suggest that different repetitive sequence families contribute significantly to the variation in genome size between indica and japonica rice, though to different extents. The increase or decrease in the copy number of several repetitive sequences examined here may indicate the existence of a directed change in genome size in rice. Possible reasons for this phenomenon of concurrent evolution of various repeat families are discussed. Received: 9 August 1999 / Accepted: 29 December 1999     

Comparative proteomic analysis of indica and japonica rice varieties

Indica and japonica are two main subspecies of Asian cultivated rice (Oryza sativa L.) that differ clearly in morphological and agronomic traits, in physiological and biochemical characteristics and in their genomic structure. However, the proteins and genes responsible for these differences remain poorly characterized. In this study, proteomic tools, including two-dimensional electrophoresis and mass spectrometry, were used to globally identify proteins that differed between two sequenced rice varieties (93–11 and Nipponbare). In all, 47 proteins that differed significantly between 93–11 and Nipponbare were identified using mass spectrometry and database searches. Interestingly, seven proteins were expressed only in Nipponbare and one protein was expressed specifically in 93–11; these differences were confirmed by quantitative real-time PCR and proteomic analysis of other indica and japonica rice varieties. This is the first report to successfully demonstrate differences in the protein composition of indica and japonica rice varieties and to identify candidate proteins and genes for future investigation of their roles in the differentiation of indica and japonica rice.     

Genetic diversity and differentiation of indica and japonica rice detected by RFLP analysis

Summary Genetic diversity and differentiation in indica and japonica groups of the cultivated rice (Oryza sativa L.) were studied by assaying DNA restriction fragment length polymorphisms of 12 indica and 14 japonica rice lines digested with three restriction endonucleases. A total of 49 probes were selected to represent the entire RFLP map at intervals of 20–30 cM. It was shown that 95 of the 145 possible probe/enzyme combinations, involving 43 probes and all three enzymes, detected restriction fragment length variation, and the degree of polymorphism varied greatly from one probe/enzyme combination to another. These results demonstrate that indica rice is genetically more diverse than japonica type. Significant differentiation between the two rice groups was detected by 33 probes representing 11 of the 12 rice chromosomes. It was deduced that the processes leading to differentiation involved a combination of molecular events that include base substitutions and insertion/deletions.     

A statistical morphological analysis and taxonomic revision of the genus Xiphophora (Fucaceae)

RICE, E. L., 1989. A statistical morphological analysis and taxonomic revision of the genus Xiphophora (Fucaceae). Xiphophora is a brown seaweed endemic to the cool temperature rocky shores of Australia and New Zealand. The two species, X. chondrophylla and X. gladiata have previously been separated by morphological criteria. However, the differences betweeen them in these characters were largely size-related, resulting in taxonomic confusion. In particular, the presence of X. gladiata in New Zealand has been disputed. In this study, a series of discriminant function analyses were performed, based on a suite of morphological characters collected from each species throughout a major portion of their geographic ranges. The results show conclusively that the present taxonomy of Xiphophora is untenable. This genus is composed of two species, but these are distributed latitudinally (either side of the 40^oS parallel). Each species contains two allopatric subspecies; one in Australia and the other in New Zealand. A formal taxonomic revision of the genus is presented.     

Genetic and heterosis analysis for cooking quality traits of indica rice in different environments

Genetic effects and genotype×environment (GE) interaction effects on the cooking quality traits of indica rice (Oryza sativa L.) were analyzed based on a genetic model for quantitative traits of triploid endosperm in cereal crops. Nine cytoplasmic male-sterile lines as females and 5 restoring lines as males were used in an incomplete diallel cross over 2 years. The cooking quality traits studied were observed to be mainly controlled by genetic effects, but GE interaction effects, especially for amylose content (AC) and alkali spreading score (ASS), were also indicated. Among the genetic effects, seed direct effects and maternal effects were the main components of AC and ASS, respectively; cytoplasmic effects were the main components of gel consistency (GC). Among the GE interaction effects, AC and ASS were mainly affected by maternal interaction effects and GC by direct interaction effects. Additive effects and/or additive interaction effects were the main factors controlling the performance of rice cooking quality traits except for GC which was affected by dominant interaction effects. For AC and GC, there were seed heterosis and/or maternal heterosis. The predicated genetic effects indicated that four parents were better than the others in improving the rice cooking quality traits of the progenies. It was shown that genetic heterosis and GE interaction heterosis were important, especially for amylose content trait in early season indica rice.     

4个太湖流域粳稻地方品种抗稻瘟病性的遗传分析

以太湖流域粳稻地方品种薄稻、铁杆青、江南晚和缺儿糯等广谱、高抗稻瘟病为材料, 与高感稻瘟病品种苏御糯杂交, 获得杂交F1、F2 , 分别接种日本稻瘟病鉴别菌系北1和中国稻瘟病菌生理小种ZE3、ZG1, 根据P1、P2、F1和F2等不同世代植株的抗、感反应, 分析地方品种对不同稻瘟病菌生理小种(菌系)的抗性遗传机理。结果表明: 薄稻、铁杆青及缺儿糯对北1菌系的抗性均可能由一对显性基因控制, 江南晚对北1的抗性则可能由两对抑制基因互作控制; 铁杆青及缺儿糯对ZE3小种的抗性均可能由一对显性基因控制, 薄稻和江南晚对ZE3小种的抗性可能分别由两对显性基因和两对抑制基因互作控制; 铁杆青对ZG1小种的抗性可能是由一对显性主基因控制, 薄稻和江南晚对ZG1小种的抗性则可能由两对抑制基因互作控制。进一步将薄稻与12个日本稻瘟病菌鉴别品种杂交,用北1菌系接种不同组合的F1和F2 , 进行抗病基因的等位性测定。结果表明, 薄稻对北1菌系的抗性基因与12个鉴别品种所携带的已知抗稻瘟病基因是不等位, 将该基因暂定为Pi-bd1(t)。     

Classification of Reynolds phytoplankton functional groups using individual traits and machine learning techniques

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Removal of the pericarp and testa of seeds of japonica and indica rice (Oryza sativa) at various oxygen concentrations has opposite effects on germination

The germination of intact, dehusked, and peeled seeds (caryopses) of the japonica rice cultivar Sasanishiki, harvested 30, 40, 47 and 60 days after anthesis, and of the indica rice cultivar Assam IV, harvested 14 and 28 days after anthesis, was examined. Dehusking strongly inhibited germination of Sasanishiki seeds, with the exception that seeds harvested 30 days after anthesis gave minimal germination percentages even when left intact. Peeling (removal of the pericarp and testa) restored or enhanced germination, and 60–100% of seeds germinated after 10 days. By contrast, the rank order of germination of Assam IV seeds was intact, dehusked, and peeled seeds, with peeled seeds yielding germination percentages of 100%. In Sasanishiki, inhibition of germination of peeled seeds was observed at reduced oxygen concentrations (1–4% oxygen). This inhibition might explain the inhibitory effects of dehusking on germination of seeds from the japonica cultivar. It is possible that the testa and pericarp, which cover the embryos of dehusked seeds, acted as a barrier to the diffusion of oxygen to the embryo.     

Comparative analysis of the 100 kb region containing the Pi-k(h) locus between indica and japonica rice lines

We have recently cloned a pathogen inducible blast resistance gene Pi-kh from the indica rice line Tetep using a positional cloning approach. In this study, we carried out structural organization analysis of the Pi-kh locus in both indica and japonica rice lines. A 100 kb region containing 50 kb upstream and 50 kb down- stream sequences flanking to the Pi-kh locus was selected for the investigation. A total of 16 genes in indica and 15 genes in japonica were predicted and anno- tated in this region. The average GC content of indica and japonica genes in this region was 53.15% and 49.3%, respectively. Both indica and japonica sequences were polymorphic for simple sequence repeats having mono-, di-, tri-, tetra-, and pentanucleotides. Sequence analysis of the specific blast resistant Pi-kh allele of Tetep and the susceptible Pi-kh allele of the japonica rice line Nipponbare showed differences in the number and distribution of motifs involved in phosphorylation, resulting in the resistance phenotype in Tetep.     

Genetic mapping of quantitative trait loci for meat quality and muscle metabolic traits in cattle

A whole‐genome scan was carried out in New Zealand and Australia to detect quantitative trait loci (QTL) for live animal and carcass composition traits and meat quality attributes in cattle. Backcross calves (385 heifers and 398 steers) were generated, with Jersey and Limousin backgrounds. The New Zealand cattle were reared and finished on pasture, whilst Australian cattle were reared on grass and finished on grain for at least 180 days. This paper reports on meat quality traits (tenderness measured as shear force at 4–5 ages on two muscles as well as associated traits of meat colour, pH and cooking loss) and a number of metabolic traits. For meat quality traits, 18 significant QTL (P < 0.05), located in nine linkage groups, were detected on a genome‐wise basis, in combined‐sire (seven QTL) or within‐sire analyses (11 QTL). For metabolic traits, 11 significant QTL (P < 0.05), located in eight linkage groups, were detected on a genome‐wise basis, in combined‐sire (five QTL) or within‐sire analyses (six QTL). BTA2 and BTA3 had QTL for both metabolic traits and meat quality traits. Six significant QTL for meat quality and metabolic traits were found at the proximal end of chromosome 2. BTA2 and BTA29 were the most common chromosomes harbouring QTL for meat quality traits; QTL for improved tenderness were associated with Limousin‐derived and Jersey‐derived alleles on these two chromosomes, respectively.     

粳稻和籼稻D1蛋白光抑制敏感性的差异与其编码基因序列结构特征的相关性分析(英文)

粳稻 (OryzasativaL .ssp .japonica)和籼稻 (O .sativassp .indica)对光抑制的敏感程度存在差异 ,它们的叶绿体光反应中心Ⅱ核心蛋白D1的稳定性不同。以菌落原位杂交法克隆了粳稻“95 16”和籼稻“籼优 6 3”叶绿体D1蛋白的编码基因psbA。核苷酸序列同源比较显示 :两者在启动子区和 5′_UTR完全相同 ;编码区存在着个别碱基的差异 ,但均位于三联体密码的第三位 ,不影响氨基酸编码特性 ,在蛋白质氨基酸序列上没有差异 ;在 3′_UTR内存在寡聚U长度的差异。因此 ,粳稻和籼稻D1蛋白对光抑制作用敏感性的差异与其蛋白质的氨基酸序列结构无关 ,可能与调控psbA基因表达的上游因子或光保护机制的差异有关。