Taxonomic status of Oryza glumaepatula Steud. II. Hybridization between New World diploids and AA genome species from Asia and Australia

Intraspecific and interspecific crosses were made using O. glumaepatula Steud., O. rufipogon Griff., O. nivara Sharma et Shastry, O. meridionalis Ng, and other diploid accessions from the New World to determine biosystematic relationships among the New World, Asian, and Australian AA genome species. All intraspecific and interspecific combinations produced seeds and hybrids, but at different levels of success. The O. glumaepatula, O. rufipogon, and O. nivara intraspecific hybrids were generally fertile with mean pollen stainability ranging from 75.2% to 80.1% and mean spikelet fertility varying from 32.1% to 87.7%. The O. meridionalis intraspecific crosses showed 3.8% pollen stainability and 0.1% spikelet fertility. Interspecific hybrids showed varying fertilities. Crosses of O. glumaepatula with the New World diploid accessions IRGC 103812 and 105561 produced highly fertile hybrids with 68.0% to 89.7% pollen stainability and 70.8% to 86.6% spikelet fertility. In crosses between O. glumaepatula and the Asian species and other diploid New World accessions IRGC 100961, 103810, and 104386, sterile hybrids were produced with pollen fertility ranging from 0 to 35.1% and spikelet fertility from 0 to 8.2%. IRGC 103810 and 104386 formed fertile hybrids when crossed to O. nivara and O. rufipogon, which were also interfertile. Interspecific crosses of O. meridionalis with the other species produced highly sterile hybrids.     

The use of RAPD markers to facilitate the identification of Oryza species within a germplasm collection

RAPD analysis was carried out using 93 accessions held within the Oryza collection in the Genetic Resource Center at IRRI. These accessions had been designated as O. meridionalis, O. glumaepatula, O. nivara or O. rufipogon on the basis of the identification of the original collector although in some cases these had been subjected to subsequent taxonomic revision. Following numerical analysis of the RAPD data, we propose that five of the forty accessions designated as O. meridionalis and four of the 22 accessions designated as O. glumaepatula have been mis-identified. The relationship between accessions designated as O. nivara and O. rufipogon is complex, although it appears that some mis-identification has also occurred for these two taxa. The results indicate that RAPD technology can be used as a fast and accurate method to assist in the validation of the identification of wild Oryza species.     

普通野生稻稻米加工品质和外观品质性状QTL定位

本研究利用一套以籼稻品种“特青”为遗传背景的云南元江普通野生稻（Oryza rufipogon Griff.）渗入系为材料，采用单标记回归分析和渗入片段叠代法，对出糙率、整精米率、垩白粒率、垩白度、长宽比等5个品质性状的QTL进行了分析，初步定位了16个QTL，有10个QTL来自野生稻的等位基因能改良群体的品质性状。在第5染色体RM289附近检测到了同时影响长宽比、垩白粒率QTL，来自野生稻的等位基因能增加长宽比、降低垩白粒率，贡献率也较高。在第8染色体RM152附近检测到降低垩白粒率和垩白度的QTL，其贡献率分别为14％和9%。本研究结果不仅为品质性状分子标记辅助选择提供参考，而且充分显示了利用野生稻的优异基因改良栽培稻品质性状的巨大潜力。     

Genetic Diversity in AA and CC Genome Oryza Species in Southern South Asia

The CC genome of Oryza is found in nine species of Oryza that are distributed on all continents having a tropical climate. Three diploid Oryza species with CC genome are found in Africa and Asia to Papua New Guinea. In southern South Asia these three CC genome diploid species can be found, O. eichingeri and O. rhizomatis in Sri Lanka and O. officinalis in India. AA genome wild relatives of rice are also found in the same geographic region. Germplasm of both diploid CC and AA genome Oryza germplasm has recently been collected from Sri Lanka. AFLP analysis was used to compare the genetic diversity of the two Oryza genomes from a similar geographic region in southern South Asia. In addition, the diploid CC Oryza germplasm was also analyzed by RAPD and SSR methodologies and the combined results were analyzed. The results show that in southern South Asia the diploid CC genome species have a high level of genetic diversity compared to the diploid AA genome species. Molecular marker analysis revealed that populations of O. rhizomatis from northern and southeastern Sri Lanka are genetically differentiated. One accession of O. rhizomatis was aligned with O. eichingeri. This accession was collected from the site of O. rhizomatis that is the closest to a population of O. eichingeri. O. eichingeri showed lower genetic diversity than the other two diploid Oryza CC genome species. O. officinalis accessions from Assam, India, and China were genetically less diverged from O. eichingeri and O. rhizomatis than two accessions of O. officinalis from Kerala state, India. The first two authors contributed equally to this research     

The Weedy Rice Complex in Costa Rica. I. Morphological Study of Relationships Between Commercial Rice Varieties,Wild <Emphasis Type="Italic">Oryza</Emphasis> Relatives and Weedy Types

Weedy rice is a complex of Oryza morphotypes widely distributed in commercial rice fields, which interfere with rice cultivation, seed production, industrial processing and commercialization of this crop in several countries. The objective of this study was to characterize the weedy rice complex of Costa Rica by comparing it with the cultivated and wild rice species found in the country. A collection of weedy rice accessions, representative of the morphotypes found in the country, was established and characterized. Their morphometric relationships were established by comparing 27 morphological traits with commercial rice cultivars, landraces and wild Oryza species and by performing a multivariate analysis. Twenty-one weedy rice morphotypes were identified among 735 weedy accessions by using a three-digit code based on seed characters. Three principal components (PCs) explained 66.25% of the variation observed. The first PC accounted for 36.21% of the variation and separated CCDD genome type Oryza latifolia and O. grandiglumis from AA genome species O. sativa, O. glumaepatula, O. rufipogon and O. glaberrima. The second (18.9%) and third (11.14%) PCs separated the weedy morphotype groups from the AA genome species O.sativa, O. glaberrima and O. rufipogon. The weedy morphotypes were scattered between the indica commercial rice varieties, the cluster landraces–glaberrima and O. rufipogon. Additionally, a group of morphotypes showed intermediate characteristics between O. sativa and O. rufipogon, suggesting that hybridization could have taken place in the past between these species. None of the morphotypes collected in Costa Rica clustered with the allotetraploids CCDD species or O. glumaepatula.     

香稻品种RVA谱多样性研究

对来自不同种植区域的593份香稻材料(香糯稻152份,香籼稻342份,香粳稻99份)进行了RVA谱的多样性分析。结果表明,香糯稻以最终粘度的变异系数最大,为42.9,香籼稻和香粳稻以回生值的变异系数最大,分别为71.9和76.1。按遗传多样性指数(Shannon-wiener多样性指数)的分级标准计算,不同种质资源RVA谱特征值的分级情况复杂,除了峰值时间分布相对集中外,其他特征值的分级情况差别较大。RVA谱各特征值的遗传多样性指数均大于1.0,香糯稻峰值粘度和最终粘度的遗传多样性指数高达2.02和2.01,香籼稻和香粳稻均以回生值的遗传指数最高,分别为2.09和1.99。不同香稻种质间的淀粉糊化特性潜在分异明显。     

Agro-morphological variation in “Jhinuwa” rice landraces (Oryza sativa L.) of Nepal

Jhinuwa is an aromatic rice (Oryza sativa L.) landrace from the Pokhara Valley of Nepal. A total of 210 accessions comprising seven types of Jhinuwa rice landraces were randomly collected from the rice fields to evaluate inter- and intra-population variability based on agro-morphological traits. The experiment was conducted in factorial randomized complete block design with three replicates in 2005. The first six principal components (PCs) accounted for 76.6 % variation for agro-morphological traits. Major traits that accounted for the variation by six PCs includes days to heading, days to maturity, total grain panicle^?1, fertile grain panicle^?1, culm length, panicle length, milling recovery, head rice recovery, aroma, 1,000 grain weight, sterile grain panicle^?1, grain sterility %, and leaf characteristics. Both principal coordinate analysis and cluster analyses revealed four phenotypic groups, two of which represent Bayarni, Jhinuwa, and Biramphul while the other two account for Tunde and Pakho Tunde. Tunde, Pakho Tunde, Kalo Bayarni, and Seto Bayarni showed higher intra- as well as inter-population variation compared to other populations. The phenotypic and genotypic coefficients of variation, broad sense heritability (h ²B) and genetic advance (GA) as a percent of the mean assessed for 210 accessions revealed high h ²B and GA estimates for leaf width, leaf length breadth ratio, ligule length, sterile grain panicle^?1, grain sterility % and 1,000 grain weight. The current study demonstrates that improvement in Jhinuwa rice landrace is possible by selecting superior accessions from existing natural populations while selection should be focussed to market traits with higher h ²B and GA estimates.     

福建漳浦野生稻稻瘟病抗性鉴定评价和抗性基因检测

为挖掘和利用福建漳浦普通野生稻稻瘟病抗性资源,采用自然诱发对福建漳浦普通野生稻2个居群(石湖潭和古糖)67份材料的苗瘟、叶瘟和穗瘟进行抗性鉴定评价,并用Pi9、Pid2、Pi5、Pi2、Pi54和Pikm共6个抗性基因的功能标记分析基因型。结果表明,不同时期病级差异明显,变异系数在31.65%~43.46%之间,苗期平均病级为7.51,分糵期和成熟期平均病级分别为5.15和5.84,2个自然居群3个时期的稻瘟病抗性差异不显著,筛选出M1044、M2010和M2016共3份表现中抗(3级)的材料。漳浦野生稻稻瘟病总体抗性差,易感稻瘟病。苗瘟与叶瘟呈极显著正相关,相关系数为0.82;穗颈瘟与苗瘟和叶瘟呈极显著正相关,相关系数分别为0.33和0.41。67份材料中,4份含有稻瘟病Pi9抗性基因、17份含有Pi5抗性基因、23份含有Pi54抗性基因、2份含有Pikm抗性基因,均不含Pi2、Pid2这2个抗性基因;材料含有的抗性基因数量在0~3个之间,其中有30份材料不含所检测的抗性基因,29份材料含1个抗性基因,7份材料含2个抗性基因,1份材料含3个抗性基因。本研究结果为漳浦野生稻资源的深入挖掘和利用提供了一定的理论参考。     

Hybridization of AA genome rice species from Asia and Australia II. Meiotic analysis of Oryza meridionalis and its hybrids

To determine the genomic constitution of Oryza meridionalis Ng (2n=2x=24) and to estimate genomic affinity between Asian and Australian wild species of rice containing the AA genomes, chromosome pairing was analyzed at metaphase I in O. meridionalis, O. rufipogon Griff. (2n=2x=24), O. nivara Sharma et Shastry (2n=2x=24), O. sativa f. spontanea Rosch, and their artifical hybrids. The Oryza parental species and their F1 hybrids showed normal meiosis, but slightly reduced chiasma fequency was observed in the hybrids. It is concluded from the cytological analysis that (i) the Australian O. meridionalis contains the AA genome which has very high affinity to that in the Asian AA genome wild species of rice; (ii) chromosome structual changes, such as inversions and reciprocal translocations, have occurred in the genomes of the different species studied.     

Genetic diversity and population structure of Capsicum baccatum genetic resources

Capsicum baccatum is one of five domesticated pepper species which, despite its morphological and ecological variability, has been underexploited for germplasm improvement. Utilizing a broad spectrum of domesticated and wild C. baccatum germplasm, we utilize AFLP markers to describe the species’ molecular diversity and population structure in the South American gene pool. Analysis of molecular variance (AMOVA) revealed greater genetic diversity in the wild form of C. baccatum (C. baccatum var. baccatum) than in the domesticated form of the species (C. baccatum var. pendulum). Both Bayesian and distance based clustering analysis, as well as principal coordinates analysis (PCA), concordantly demonstrated admixture/shared ancestry between wild and cultivated C. baccatum botanical varieties. Two principal genetic groups were identified in the domesticated C. baccatum accessions largely based on their geographic distribution in South America. One group was predominated by accessions from the western territories of the species’ distribution (Peru, Colombia, Ecuador, Bolivia, Chile and northwestern Argentina) and the second by accessions from the eastern regions, Paraguay and eastern Argentina). The two genetic groups overlapped in the geographic location of present-day Bolivia. The grouping pattern suggested that C. baccatum was domesticated in multiple sites and that its evolution took two lineages followed by lineage differentiation. The wild accessions most closely related to the cultigens were found in the highlands of Peru and Bolivia, which support the early hypothesis that this region is one of the domestication sites of this species. A Bayesian assignment analysis demonstrated that Brazilian wild forms of C. baccatum were genetically distant to all other accessions and made little to no contribution to the domesticated genepool. Moreover, results of clustering analysis suggested that C. baccatum likely originated from present day Paraguay. Analysis of inter-specific relationships across selected Capsicum species supported independent lineages for the two crossability groups within Capsicum, the baccatum species-complex (including C. baccatum) and the annuum species-complex (including C. annuum, C. chinense and C. frutescens). However, the results did not support taxonomic distinction of C. baccatum var. umbilicatum from C. baccatum var. pendulum. The present study provides new insights into the domestication of C. baccatum. The results will be useful for identifying accessions for crop improvement and guiding the development of in situ and ex situ conservation programs.     

Hybridization of AA genome rice species from Asia and Australia I. Crosses and development of hybrids

Interspecific and intraspecific crosses of rice species were made involving the AA genome wild species Oryza meridionalis Ng from Australia, O. nivara Sharma et Shastry, O. rufipogon Griff, the weedy type O. sativa f. spontanea Rosch., and the cultigen O. sativa L. from Asia. Seed set and the number of hybrids obtained from both interspecific and intraspecific crosses were low and no significant differences were observed between the interspecific and intraspecific crosses. In the combination O. meridionalis × O. nivara and O. meridionalis × O. rufipogon, considerable differences in reciprocal crosses were observed, whereas higher seed set and more hybrids were obtained when O. meridionalis was used as the female parent. Pollen stainability and seed fertility of hybrids were very low, averaging between 1% and 9% in both interspecific and intraspecific combinations, except in the O. nivara intraspecific cross of 105386 × 106111, whose hybrid showed 83.0% pollen stainabi lity and 66.5% seed fertility.     

Genetic diversity of African wild rice (Oryza longistaminata Chev. et Roehr) at the edge of its distribution

Ethiopia is at the edge of the distribution for African wild rice, Oryza longistaminata. Here, chloroplast (cp) and simple sequence repeat (SSR) markers were applied to wild rice accessions in Ethiopia to evaluate how they differ from control O. longistaminata, O. barthii and O. glaberrima accessions which originated from African countries. Based on the cp genomes of African wild rice species, maternally inherited cpINDEL markers were developed. The cp indels helped to elucidate 20 plastid types. African cultivated rice shared a particular plastid type with one of annual O. barthii. Parts of northern wild rice in Ethiopia shared Type 6 with control O. longistaminata. The north group shared another type with parts of the south group. The 16 SSR markers amplified a total of 155 alleles in 215 rice accessions, with mean allelic richness of 9.688 per locus, observed heterozygosity of 0.241, expected heterozygosity of 0.724, polymorphic information content of 0.700, and a significant genetic differentiation of 0.215. Both cpINDEL and nuclear markers analyses suggested that wild rice in Ethiopia belongs to O. longistaminata. However, they carry both a unique plastid type and different population structure from control O. longistaminata collected from other areas in Africa. We concluded that the edge of its distribution maintains unique variation. These populations are regarded as valuable genetic resources for future rice breeding.

     

Identification of <Emphasis Type="Italic">SUB1A</Emphasis> alleles from wild rice <Emphasis Type="Italic">Oryza rufipogon</Emphasis> Griff.

Submergence stress is a major constraint to rice production in South and Southeast Asia. Most rice (Oryza sativa L.) cultivars die within a week of complete submergence, while a small number of accessions are submergence-tolerant for up to 2 weeks or more. These cultivars have the tolerant allele of the SUB1A gene, one of three ERF genes at this locus on rice chromosome 9. In all O. sativa varieties studied, the SUB1A gene is limited to a subset of indica accessions of O. sativa. Thus far, there has been no published report of the SUB1A gene in wild rice species. Here we report evidence of the SUB1A gene found in wild species of O. rufipogon Griff. accessions by the use of degenerate primers corresponding to the most highly conserved regions of the SUB1 locus. The results indicated that two SUB1A-like alleles, e.g. OrSub1A-1 and OrSub1A-2, were identified from two O. rufipogon accessions. Submergence treatment shows that both of the accessions with SUB1A-like genes were submergence-intolerant. This preliminary study provides insight into the origin and allelic variation of SUB1A, an agronomically important gene that is rapidly being introduced into widely-grown rice cultivars.     

The fragrance (fgr) gene in natural populations of wild rice (Oryza rufipogon Griff.)

The Asian cultivated rice, Oryza sativa L. (spp. indica or japonica), is assumed to have originated from one or both of the two wild Asian species, O. rufipogon Griff. and O. nivara Sharma and Shastry. They occur throughout the monsoon Asia and west Oceania. Fragrance is the most important trait among the domesticated characters of basmati and jasmine rice of Asia. The gene for fragrance in a scented rice shows the presence of a mutated portion (i.e., an eight base pair deletion in exon 7) that result in its loss of fragrance. In the present study, 229 wild rice O. rufipogon accessions were genotyped for this locus using a PCR assay. The wild rice species contained the mutated allele of the fgr gene at a low frequencies of 0.23. The surveyed populations were in Hardy–Weinberg equilibrium. This observation supports the hypothesis that the allele for fragrance was already present in the wild rice, and that this trait appeared in scented rice cultivars because of selection by the farmers of genotypes possessing this character during the process of domestication.     

Genetic diversity and species delimitation in the cultivated and wild Guinea yams (Dioscorea spp.) from Southwest Ethiopia as determined by AFLP (amplified fragment length polymorphism) markers

Yams (Dioscorea spp.) rank as the fourth most important root and tuber crop after potatoes, cassava and sweet potatoes. They are an economic crop in most of the tropics especially in West Africa, which produces over 95 % of the world output. Despite their cultural and economic importance there is taxonomic confusion regarding Guinea yams. The currently used classification scheme, which relies on vegetative and inflorescence characters, does not consistently delimit species boundaries between members of Guinea yams (D. cayenensis Lam.–D. rotundata Poir. complex), their wild relatives (D. abyssinica Kunth and D. praehensilis Benth.,) and D. sagittifolia Pax. Establishing the taxonomic identity of the germplasm and understanding the systematic relationships among crops is vital to the management of genetic resources and the utilization of accessions. In this study, amplified fragment length polymorphism (AFLP) genetic fingerprinting was used to evaluate and characterize 43 individual plants, belonging to different populations of wild and cultivated Guinea yams. The three primer combinations used in the AFLP analyses generated 158 scorable bands, with an overall polymorphism of 78 %. Ordination and cluster analyses of AFLP data failed to produce any clear species boundary between either the Guinea yam accessions or between them and their wild relatives. The average genetic similarity between the study individuals of Guinea yams and their wild relatives ranged from 60 to 100 %. The first, second and third principal coordinates axes cumulatively account for 77.45 % of the total variation. AFLP analyses also revealed a higher genetic divergence among cultivated Guinea yam accessions of the Sheko cultivars. Ordination and cluster analysis using UPGMA revealed no clear species boundaries between members of the complex. Thus, the taxonomy of these “species” needs to be revisited using other markers.     

Collection of Lupinus angustifolius L. Germplasm and Characterisation of Morphological and Molecular Diversity

Lupinus angustifolius L. is a Mediterranean species, domesticated in the 20th century, representing an important grain legume crop in Australia and other countries. This work is focused on the collection of wild germplasm and on the characterisation of morphological and molecular diversity of germplasm accessions. It reports the collection of 81 wild L. angustifolius accessions from the South and Centre of Portugal, available at the ‘Instituto Superior de Agronomia Gene Bank’, with subsequent morphological and molecular characterisation of a selection of these and other accessions. A multivariate analysis of morphological traits on 88 L. angustifolius accessions (including 59 wild Portuguese accessions, 15 cultivars and 14 breeding lines) showed a cline of variation on wild germplasm, with plants from Southern Portugal characterised by earlier flowering, higher vegetative development and larger seeds. AFLP and ISSR molecular markers grouped modern cultivars as sub-clusters within the wider diversity of wild germplasm, revealing the narrow pool of genetic diversity on which domesticated accessions are based. The importance of preserving, characterising and using wild genetic resources for L. angustifolius crop improvement is outlined by the results obtained.     

Diversity analysis and evaluation of wild <Emphasis Type="Italic">Abelmoschus</Emphasis> species for agro-morphological traits and major biotic stresses under the north western agro-climatic condition of India

The wild species in general is considered to be the reservoir of genes especially for biotic and abiotic stresses. In okra, the predominant biotic stresses are yellow vein mosaic disease (YVMD), shoot and fruit borer and leaf hopper. Sixty eight (68) accessions belonging to four wild Abelmoschus species [Abelmoschus caillei (A. Chev.) Stevels, Abelmoschus manihot (L.) Medik., Abelmoschus moschatus (L.) Medik. and Abelmoschus tuberculatus Pal et Singh] and eight okra varieties were characterized and evaluated for phenological characters including biotic stresses under natural epiphytotic condition. The wild species examined consisted of 18 accessions (16 exotic and 2 indigenous) of A. caillei, 29 accessions of A. manihot, 16 accessions of A. moschatus and 5 accessions of A. tuberculatus. All the wild Abelmoschus species exhibited high diversity (as measured by Shannon Diversity Index) for 3 qualitative characters viz. intensity of stem colour, leaf shape, epicalyx shape, 13 quantitative characters and 3 biotic stress parameters. Among the wild species, A. caillei and A. tuberculatus showed maximum and minimum diversity for qualitative characters, respectively. There was significant variation for 19 out of 24 quantitative characters studied. Inter-species diversity pattern as estimated through Ward’s Minimum Variance Dendrogram and Principal Component Analysis revealed clear differentiation among the species with minimum overlapping indicating close association between geographical origins and clustering pattern. Intra-species diversity indicated role of specific adaptation in sub-clustering. Resistance to YVMD was found in accessions belonging to three wild species viz. A. caillei, A. manihot and A. moschatus while resistance to shoot and fruit borer and leaf hopper was found in accessions of all the four wild species. The resistant accessions can further be used for introgressing biotic stress resistance through pre-breeding into cultivated okra species.     

Genetic diversity and origin of cultivated potatoes based on plastid microsatellite polymorphism

The origin of cultivated potatoes has remaining questions. In this study, 237 accessions of all cultivated species and 155 accessions of wild species closely related to cultivated potatoes, including their putative ancestors, were analyzed using 15 plastid microsatellites (SSRs) to investigate genetic diversity and their relationships with the wild species. We here used polymorphic plastid SSRs we developed from potato plastid genome sequences as well as already known plastid SSR markers. All 15 loci were polymorphic and identified a total of 127 haplotypes. Dramatic decreases in levels of genetic diversity were revealed in landraces in comparison with wild ancestor species. The plastid SSR results showed a decrease in haplotype number and diversity from Peru to both north and south. Phylogenetic analysis revealed two distinct groups. One of them, group A, contained the majority of accessions of cultivated species of the Solanum tuberosum Andigenum group including all accessions of cultivated diploid and triploid cytotypes of this group (S. chaucha, S. phureja, and S. stenotomum by a former taxonomic system) and most of tetraploid accessions of the S. tuberosum Andigenum group (S. tuberosum subsp. andigenum), and the majority of accessions of wild ancestors from the northern members of the S. brevicaule complex. Another group B comprised most of the wild species accessions and almost exclusively hybrid cultivated species which have introgressed plastid genomes from the other wild gene pools. Lack of clustering of traditional cultivated species (as used above) support a revised group classification of S. tuberosum.     

Variation in a wild groundnut species, Arachis duranensis Krapov. & W.C. Gregory

Forty-two accessions of Arachis duranensis, a wild groundnut species that has been reported as a source of resistance to several groundnut diseases, were studied for 30 quantitative traits including total protein content, oil content, and reaction to groundnut rust. Protein profiles were also investigated for variation at the molecular level. Principal component analysis was applied to 28 traits that showed significant variation. Of these, only five characters, namely, height of the main stem, length of apical leaflet on the main stem, length of isthmus between pods, width of seed, and reaction to groundnut rust, accounted for more than 61.4% of the total variation. Protein profiles of these accessions were broadly similar, except some accessions which differed in few bands. The importance of these variations in strategies for germplasm collection and breeding is discussed.Submitted as Journal Article No. 1507 by the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru P.O. 502 324 A.P. India.