Molecular Mapping of QTLs for Yield and Yield-Related Traits in Oryza sativa cv Swarna × O. nivara (IRGC81848) Backcross Population

Advanced backcross QTL analysis was used to identify QTLs for seven yield and yield-related traits in a BC2F2 population from the cross between a popular Oryza sativa cv Swarna and O. nivara IRGC81848. Transgressive segregants with more than 15% increased effect over Swarna were observed for all the traits except days to heading and days to 50% flowering. Thirty QTLs were detected for seven yield and yield-related traits using interval and composite interval mapping. Enhancing alleles at 13 (45%) of these QTLs were derived from O. nivara, and enhancing alleles at all the QTLs for stem diameter and rachis diameter were derived from O. nivara. Three stem diameter QTLs, two rachis diameter QTLs and one number of secondary branches QTL identified by both Interval and composite interval mapping contributed more than 15% of the total phenotypic variance. The QTL epistasis was significant for stem diameter and plot yield. The most significant QTLs qSD7.2, qSD8.1 and qSD9.1 for stem diameter, qRD9.1 for rachis diameter and qNSB1.1 for number of secondary branches are good targets to evaluate their use in marker-assisted selection. O. nivara is a good source of novel alleles for yield related traits and reveals major effect QTLs suitable for marker-assisted selection.

Yield Traits and Associated Marker Segregation in Elite Introgression Lines Derived from O. sativa × O. nivara

Introgression lines(ILs)derived from interspecific crosses are a source of new genetic variability.A total of 55 ILs derived from two crosses Swarna×O.nivara IRGC81848(population A)and Swarna×O.nivara IRGC81832(population B)were characterized for yield and yield-related traits/QTLs.Segregation of 103 simple sequence repeat(SSR)markers associated with yield-related QTLs was studied.Population A showed an average of 12.6%homozygous O.nivara alleles and population B showed 10.6%.Interestingly,three SSR markers,RM223,RM128 and RM517,showed conspicuous pattern of segregation.The distribution of parental alleles at three loci RM223,RM128 and RM517 linked to yield-related traits was unique.These markers flanked to several yield-related QTLs.RM223,flanking to qyld8.3,was heterozygous in almost all the 55 ILs except in IL10-3S and IL131S.RM128 on chromosome 1 and RM517 on chromosome 3 were mutually exclusive in 46 out of 55 ILs.These 46 ILs showed either of the marker allele RM128 or RM517 from O.nivara but not both.IL166S had both RM128and RM517 from O.nivara and the other ILs showed homozygous Swarna allele at RM517 except IL65S.Population structure assigned the 55 ILs to three sub-populations based on their genomic diversity.IL65S,IL166S,IL248S,IL7K and IL250K showed high yields in multi-location trials,and IL248S was released for cultivation as DRRDhan 40.

Environmental Factors Undermine Genetic Expression of Tiller Dynamics in Wild Rice <i>Oryza nivara</i>and <i>Oryza rufipogon</i>

Tillering is a principal trait for the study of branching and production of more number of panicles for increased grain production in many cereal crops. Most of the semi-dwarf high yielding rice cultivars exhibit a remarkable degree of stability with respect to their tillering ability and maintain almost a constant tiller number which is genetically fixed for a particular cultivar. However, tiller production in wild species of rice is largely determined by environmental parameters, which supersede genetic features for expression of complete tillering ability. Two species of wild rice like Oryza nivara and Oryza rufipogon were tested for influence of manipulated growing conditions on tiller dynamics by comparing their growth in natural habitats and cemented pots filled with manure added soil. The results revealed a significant enhancement in the number of tiller production as well as biomass accumulation of each tiller with more grain yield in the cultivated conditions in both the species in comparison to the wild situations. The dryland inhabitant O. nivara became mono-tillering and deep water species O. rufipogon produced as many as five tillers with relatively lesser grain yield in their natural environments compared to their cultivated counterparts. From these observations, it is concluded that expression of genetic potential for tiller production is amenable to fluctuation of environmental factors in the wild species of rice and their capacity for adaption to inclement growth conditions.

Donors for Resistance to Brown Planthopper Nilaparvata lugens(St?l) from Wild Rice Species

Out of 1 989 wild accessions sown in seed boxes for screening, only 1 003 wild accessions with good germination were screened against brown planthopper(BPH), Nilaparvata lugens(St?l) under greenhouse conditions. The collection comprised of accessions from 11 wild species and African cultivated rice. The germplasm was screened for BPH following standard seed box screening technique in the greenhouse. As many as 159 accessions were identified as resistant during the year 2012 based on one year screening. A selected set of BPH resistant accessions were screened again during 2013. Based on the two years screening, seven accessions of O. nivara(AA), one accession of O. officinalis(CC), seven accessions of O. australiensis(EE), five accessions of O. punctata(BB and BBCC) and nine accessions of O. latifolia(CCDD) were confirmed to be resistant to BPH. So far no BPH resistance genes have been identified and designated from O. nivara and O. punctata, hence these may act as new sources of resistance.

Seed Length Controlled by Same Locus in Four Different AA Genome Species of Genus Oryza

To broaden the genetic basis and overcome the yield plateau in Asian cultivated rice, the exploitation and utilization of favorable alleles from rice species with the AA genome has become important and urgent in modern breeding programs. Four different interspecific populations were used to detect quantitative trait locus （QTL） for seed length, including a BC4F2 population derived from Oryza glumaepatula crossed with Dianjingyou 1 （a japonica cultivar）, a BC4F2 population derived from O. nivara crossed with Dianjingyou 1, a BCzF1 population derived from a cross between O. Iongistaminata and RD23 （an indica cultivar）, and a BCsF1 population derived from a cross between O. glaberrima and Dianjingyou 1. The QTLs for seed length in four different populations were termed as SL-3a, SL-3b, SL-3c and SL-3d, respectively. They had good collinearity and accounted for 49% to 60% of the phenotypic variations. Sequencing data indicated that four QTLs were different alleles of GS3 which were responsible for the seed length variation between O. sativa and its four AA genome relatives. These results will be valuable for confirming the evolution of GS3 and also be helpful for rice breeding.

尼瓦拉野生稻(Oryza nivara)小粒基因GS3-N的克隆及功能分析

水稻粒型是影响产量的一个重要因素,为挖掘和利用野生稻中粒型相关基因并解析其功能机制,本研究以尼瓦拉野生稻(Oryza nivara)为供体亲本,粳稻品种‘滇粳优1号’(DJY1)为轮回亲本,构建了一个极小粒近等基因系NIL-J155。图位克隆获得了尼瓦拉野生稻中负调控籽粒大小的GS3基因的一个新的单倍型,命名为GS3-N(GS3 from O.nivara)。GS3-N定位在细胞膜,且在不同生长阶段的不同组织中均有表达。序列分析表明,小粒单倍型GS3-NJ155第5个外显子处有312 bp的插入和缺失,其编码的蛋白含有植物特有的器官大小调控区(OSR)和跨膜结构域,而大粒单倍型GS3-NDJY1由于第2个外显子处的无义突变,导致编码蛋白只含有部分OSR结构域。进一步的研究表明,在J155背景下分别敲除OSR和跨膜结构域都能显著增加其粒长和粒重,过表达植株则表现粒长明显变短,株高降低,穗长变短,证明GS3-N可能具有一因多效的作用。本研究结果表明作为调控粒长的负调节子,GS3-N编码蛋白和转录表达水平的差异是引起J155和DJY1粒型差异的原因,这不仅为水稻粒型驯化机制提供新的理论基础,还将为现代水稻栽培种提供更多的粒型遗传资源。

转基因水稻与野生稻(Oryza nivara Sharma et Shastry)杂交后代种子萌发率

种子休眠性是野生植物重要的适应性状,通过种子萌发实验可以分析种子休眠性强弱.通过人工杂交获得转抗虫基因栽培稻与一年生普通野生稻三种组合的杂种,对杂种的F3代和F4代种子采用直接萌发、打破休眠后萌发、埋土15 d和30 d 4种不同处理来检测种子活力和萌发率.结果显示转基因杂种后代种子表现出较强的休眠性,转基因对种子活力和休眠性没有明显的影响,种子休眠性有随种子世代的增加而逐渐减弱的趋势,提示水稻转基因逃逸后有在野生稻群体中宿存和扩散的可能性,但这种可能性可能会随世代增加而下降.这为进一步研究水稻转基因逃逸风险提供了参考.

水稻S5^n基因的分子进化及功能比较

S5n基因是克服水稻亚种间杂种胚囊不育性最主要因子之一,了解其序列特征对于揭示其起源或进化以及在分子育种上的应用具有重要意义.本文以48份携带有S5n的栽培稻品种和野生稻为材料,通过对其S5n的全序列进行测定,并选择在编码区序列差异较大的品种(系)与籼粳测验种进行测交组配F1,研究不同序列S5n在克服水稻亚种间杂种胚囊不育性效应的差异.结果表明,48份材料的DNA全序列与对照02428完全一致的有15份,其他33份存在不同程度的变异.变异位点,包括颠换、转换和缺失等,共有24个.编码区的变异主要发生在外显子2,其中变异最大的8份材料在1710～1719bp处缺失了10个碱基,包括尼瓦拉野稻IRW501和栽培稻品种粤泰B等.S5n序列变异没有偏向性,说明S5n是中性进化基因.通过构建S5n全序列及其编码区编码氨基酸系统NJ树,将48份材料归为4类,其中大部分的栽培稻聚成一类,普通野生稻聚成一类,8份缺失10个碱基的材料聚为一类,其他的材料聚成一类.利用WE-CLSM(whole-mount eosin B-staining confocal laser scanning microscopy)对测交F1的胚囊育性观察表明,不同S5n序列材料组配测交F1的胚囊育性均比对照明显增加,彼此间没有显著差异,显示它们都能克服亚种间的胚囊不育性,也间接证明S5n是功能缺失基因.

尼瓦拉野生稻内生菌多样性和促生作用

为从尼瓦拉野生稻（Oryza nivara）中收集农业微生物肥料生产的菌种资源,对其内生菌进行分离、固氮酶活性测定、IS-PCR指纹图谱聚类、产生长素、解钾能力及生理生化特性测定.选取IS-PCR指纹图谱8个类群的代表菌株进行16S rRNA基因系统发育分析.从尼瓦拉野生稻中共分离到57株内生细菌,其中44株为内生固氮菌,固氮酶活性在5.79-899.72 nmol mL^（-1） h^（-1）之间.16S rRNA基因序列分析及生理生化特性表明,所分离的植物内生菌属于Burkholderia contaminans、Herbaspirillum seropedicae、Rhizobium sp.、Bacillus methylotrophicus、Achromobacter xyosoxidan、Chryseobacterium bernardeti、Pseudomonas beteli和Klebsiella quasipneumoniae,表明尼瓦拉野生稻内生菌具有多样性.分离到的内生细菌均有产生长素的能力,其中N8、N35、N36产生长素能力最强,分别为41.66、34.96、30.41 mg∕L.25株菌株具有不同程度的解钾能力,N37、N16解钾能力最强,分别为312、289 mg/L.N8、N35、N36、N37、N16接种生菜后,生菜株高增加12.47%-26.17%、叶片数增加20.41%-44.90%、叶长增长49.73%-62.23%、地上鲜重增加37.93%-68.00%、地下鲜重增加31.08%-40.56%、叶绿素含量增加27.94%-85.29%.接种菌株N37、N16的土壤与对照组相比,土壤速效钾含量分别增加52.55%和57.85%,表明菌株具有明显的促生效果.综上所述,从尼瓦拉野生稻中筛选到的5株多功能促生菌在未来农业微生物肥料生产应用上具有潜在的价值.

The Puzzle of Rice Domestication

The origin of cultivated rice has puzzled plant biologists for decades. This is due, at least in part, to the complex evolutionary dynamics in rice cultivars and wild progenitors, particularly rapid adaptive differentiation and continuous gene flow within and between cultivated and wild rice. The long-standing controversy over single versus multiple and annual versus perennial origins of cultivated rice has been brought into shaper focus with the rapid accumulation of genetic and phylogenetic data. Molecular phylogenetic analyses revealed ancient genomic differentiation between rice cultivars, suggesting that they were domesticated from divergent wild populations. However, the recently cloned domestication gene sh4, responsible for the reduction of grain shattering from wild to cultivated rice, seems to have originated only once. Herein, we propose two models to reconcile apparently conflicting evidence regarding rice domestication. The snowoballing model considers a single origin of cultivated rice. In this model, a core of critical domestication alleles was fixed in the founding cultivar and then acted to increase the genetic diversity of cultivars through hybridization with wild populations. The combination model considers multiple origins of cultivated rice. In this model, Initial cultivars were domesticated from divergent wild populations and fixed different sets of domestication alleles. Subsequent crosses among these semi-domesticated cultivars resulted in the fixation of a similar set of critical domestication alleles in the contemporary cultivars. In both models, introgression has played an important role in rice domestication. Recent and future introgression of beneficial genes from the wild gene pool through conventional and molecular breeding programs can be viewed as the continuation of domestication.

Molecular evolution of rice S_5~n and functional comparison among different sequences

The wide compatibility gene, S 5 n , can overcome embryo sac sterility between indica and japonica subspecies of rice. Therefore, it is very important to characterize the features of the S 5 n sequence to reveal the origin and evolution of S 5 n . In this paper, 26 cultivated rice haplotypes and 22 wild rice accessions harboring S 5 n were used to sequence S 5 n . The results showed that 15 genotypes among the 48 materials were fully consistent with control cultivar 02428 (CK). The other 33 accessions had different degrees of variation in the S 5 n sequence. Variations in the coding region mainly occurred in the second exon and eight materials showed a 10-bp deletion at 1710–1719 bp, including wild (O. nivara) and cultivated rice, such as IRW501 and Yuetai B. S 5 n sequences were not biased and evolved neutrally. The 48 materials could be divided into 4 categories using a phylogenetic tree of the amino acid sequences. Most of the wild rice clustered together, and the cultivated rice clustered into another group. Eight cultivated rice and O. nivara (wild rice) clustered in another group, which were found to lack 10 consecutive bases in exon 2. Eight rice varieties with high numbers of differences in their S 5 n coding regions were crossed with testers (typically indica and japonica) to produced test cross F 1 populations. The F 1 s were examined for their ability to overcome indica-japonica hybrid sterility. The result showed that the embryo sac fertility of S 5 n -containing hybrids increased significantly compared with control hybrids, but there were no differences among the materials with divergent sequences, indirectly proving that S 5 n is a non-functional gene.