Rphq2, a minor gene for partial resistance to Puccinia hordei , was physically mapped in a 188 kbp introgression with suppressed recombination between haplotypes of rphq2 and Rphq2 barley cultivars.
KEY MESSAGE: We developed 'Golden SusPtrit', i.e., a barley line combining SusPtrit's high susceptibility to non-adapted rust fungi with the high amenability of Golden Promise for transformation. Nonhost and partial resistance to Puccinia rust fungi in barley are polygenically inherited. These types of resistance are principally prehaustorial, show high diversity between accessions of the plant species and are genetically associated. To study nonhost and partial resistance, as well as their association, candidate gene(s) for resistance must be cloned and tested in susceptible material where SusPtrit would be the line of choice. Unfortunately, SusPtrit is not amenable to Agrobacterium-mediated transformation. Therefore, a doubled haploid (DH) mapping population (n = 122) was created by crossing SusPtrit with Golden Promise to develop a 'Golden SusPtrit', i.e., a barley line combining SusPtrit's high susceptibility to non-adapted rust fungi with the high amenability of Golden Promise for transformation. We identified nine genomic regions occupied by resistance quantitative trait loci (QTLs) against four non-adapted rust fungi and P. hordei isolate 1.2.1 (Ph.1.2.1). Four DHs were selected for an Agrobacterium-mediated transformation efficiency test. They were among the 12 DH lines most susceptible to the tested non-adapted rust fungi. The most efficiently transformed DH line was SG062N (11-17 transformants per 100 immature embryos). The level of non-adapted rust infection on SG062N is either similar to or higher than the level of infection on SusPtrit. Against Ph.1.2.1, the latency period conferred by SG062N is as short as that conferred by SusPtrit. SG062N, designated 'Golden SusPtrit', will be a valuable experimental line that could replace SusPtrit in nonhost and partial resistance studies, especially for stable transformation using candidate genes that may be involved in rust-resistance mechanisms.
Oil palm (Elaeis guineensis Jacq.) requires 19 years per cycle of phenotypic selection. The use of molecular markers may reduce the generation interval and the cost of oil-palm breeding. Our objectives were to compare, by simulation, the response to phenotypic selection, marker-assisted recurrent selection (MARS), and genomewide selection with small population sizes in oil palm, and assess the efficiency of each method in terms of years and cost per unit gain. Markers significantly associated with the trait were used to calculate the marker scores in MARS, whereas all markers were used (without significance tests) to calculate the marker scores in genomewide selection. Responses to phenotypic selection and genomewide selection were consistently greater than the response to MARS. With population sizes of N = 50 or 70, responses to genomewide selection were 4-25% larger than the corresponding responses to phenotypic selection, depending on the heritability and number of quantitative trait loci. Cost per unit gain was 26-57% lower with genomewide selection than with phenotypic selection when markers cost US $1.50 per data point, and 35-65% lower when markers cost $0.15 per data point. With population sizes of N = 50 or 70, time per unit gain was 11-23 years with genomewide selection and 14-25 years with phenotypic selection. We conclude that for a realistic yet relatively small population size of N = 50 in oil palm, genomewide selection is superior to MARS and phenotypic selection in terms of gain per unit cost and time. Our results should be generally applicable to other tree species that are characterized by long generation intervals, high costs of maintaining breeding plantations, and small population sizes in selection programs.
The genetic diversity of 255 taro (Colocasia esculenta) accessions from Vietnam, Thailand, Malaysia,Indonesia, the Philippines, Papua New Guinea and Vanuatu was studied using AFLPs. Three AFLP primer combinations generated a total of 465 scorable amplification products. The 255 accessions were grouped according to their country of origin, to their ploidy level (diploid or triploid) and to their habitat--cultivated or wild. Gene diversity within these groups and the genetic distance between these groups were computed. Dendrograms were constructed using UPGMA cluster analysis. In each country, the gene diversity within the groups of wild genotypes was the highest compared to the diploid and triploid cultivars groups. The highest gene diversity was observed for the wild group from Thailand (0.19), the lowest for the diploid cultivars group from Thailand(0.007). In Malaysia there was hardly any difference between the gene diversity of the cultivars and wild groups, 0.07 and 0.08, respectively. The genetic distances between the diploid cultivars groups ranges from 0.02 to 0.10, with the distance between the diploid accessions from Thailand and Malaysia being the highest. The genetic distances between the wild groups range from 0.05 to 0.07. First, a dendrogram was constructed with only the diploids cultivars from all countries. The accessions formed clusters largely according to the country from which they originated. Two major groups of clusters were revealed, one group assembling accessions from Asian countries and the other assembling accessions from the Pacific. Surprisingly, the group of diploid cultivars from Thailand clustered among the Pacific countries. Secondly,a dendrogram was constructed with diploid cultivated,triploid cultivated and wild accessions. Again the division of the accessions into an Asian and a Pacific gene pool is obvious. The presence of two gene pools for cultivated diploid taro has major implications for the breeding and conservation of germplasm.
A total of 723 accessions of oil palm ( Elaeis guineensis Jacq.) from 26 populations representing ten countries in Africa and one Deli dura family were screened for allelic variation at seven enzyme loci from six enzyme systems using starch gel electrophoresis. On average, 54.5% of the loci were polymorphic (0.99 criterion). The average and effective number of alleles per locus was 1.80 and 1.35, respectively. Mean expected heterozygosity was 0.184, with values ranging from 0.109 (population 8, Senegal) to 0.261 (population 29, Cameroon). The genetic differentiation among populations was high (F(ST)=0.301), indicating high genetic divergence. The calculation of F(ST) by geographic zones revealed that the high F(ST) was largely due to F(ST) among populations in West Africa, suggesting diversifying selection in this region. The mean genetic distance across populations was 0.113. The lowest genetic distance (D) was observed between population 5 from Tanzania and population 7 from the Democratic Republic of the Congo (0.000) and the highest was found between population 4 from Madagascar and population 13 from Sierra Leone (0.568). The total gene flow across oil palm populations was low, with an Nm of 0.576, enhancing genetic structuring, as evident from the high F(ST) values. UPGMA cluster analysis revealed three main clusters; the western outlying populations from Senegal and Sierra Leone were in one cluster but separated into two distinct sub-clusters; the eastern outlying populations from Madagascar were in one cluster; the populations from Angola, Cameroon, The Democratic Republic of the Congo, Ghana, Tanzania, Nigeria and Guinea were in one cluster. The Deli dura family seems to be closely related to population 6 from Guinea. Oil palm populations with high genetic diversity-i.e. all of the populations from Nigeria, Cameroon and Sierra Leone, population 6 of Guinea, population 1 of Madagascar and population 2 of Senegal should be used in improvement programmes, whereas for conservation purposes, oil palm populations with high allelic diversity (A(e)), which include populations 22 and 29 from Cameroon, populations 39 and 45 from Nigeria, population 6 from Guinea, populations 5 and 13 from Sierra Leone and population 1 from Madagascar should be selected for capturing as much genetic variation as possible.
The genetic differentiation of nuclear, mitochondrial (mt) and chloroplast (cp) genomes was investigated by Southern and PCR analysis using 75 varieties of cultivated rice ( Oryza sativa L.) and 118 strains of common wild rice (CWR, Oryza rufipogon Griff.) from ten countries of Asia. The distinguishing differences between the Indica and Japonica cultivars were detected both in the nuclear genome and the cytoplasmic genome, confirming that the Indica-Japonica differentiation is of major importance for the three different classes of genome in cultivated rice. This differentiation was also detected in common wild rice with some differences among the genome compartments and the various regions. For nuclear DNA variation, both Indica-like and Japonica-like types were observed in the Chinese CWR, with the latter more-frequent than the former. No Japonica-like type was found in South Asia, and only two strains of the Japonica-like type were detected in Southeast Asia, thus the Indica-like type is the major type among South and Southeast Asian CWR. For mtDNA, only a few strains of the Japonica-like type were detected in CWR. For cpDNA, the Japonica type was predominant among the CWR strains from China, Bangladesh and Burma, while the Indica type was predominant among the CWR strains from Thailand, Malaysia, Cambodia and Sri Lanka, and both types were found in similar frequencies among the Indian CWR. Altogether, however, the degree of Indica-Japonica differentiation in common wild rice was much-less important than that in cultivated rice. Cluster analyses for nuclear and mitochondrial DNA variation revealed that some CWR strains showed large genetic distances from cultivated rice and formed clusters distinct from cultivated rice. Coincidence in the genetic differentiation between the three different classes of genome was much higher in cultivated rice than in CWR. Among the 75 cultivars, about 3/4 entries were "homoeotype" showing congruent results for nuclear, mt and cpDNA regarding the Indica-Japonica differentiation. In CWR, the proportions of homoeotypes were 5.7%, 15% and 48.8% in China, South Asia and Southeast Asia, respectively. Based on the average genetic distance among all the strains of CWR and cultivated rice for nuclear and mitochondrial genomes, the variability of the nuclear genome was found to be higher than that of the mitochondrial genome. The global pattern based on all genomes shows much-more diversification in CWR than that in cultivated rice.
The genetic variation among different accessions of oil-palm germplasm collected from Africa was estimated using random primers and the polymerase chain reaction. The present study revealed high levels of genetic variation in these accessions. Electrophoresis of the amplification products indicated that nine out of 20 primers were able to generate polymorphic products ranging in length from 0.2 kb to 2.3 kb. No individual palm or population-specific products were observed. Greatest diversity was seen in Zaire population 5 and the least in Zaire population 2.
CONCLUSIONS: The comparison of different selection indices is justified only if the indices are constrated to achieve the same profit function, even when each index is not optimized with respect to that profit function.When a profit function is known and is non-linear, the desired gains index may be more efficient than the economic index. The optimum desired gains index should be determined by iterative techniques over several generations to compare the genetic progress with the economic index, because gains by the economic index are not linear and the changes observed in the initial generations of selection are not the same rates in future generations, although those changes are linear in the case of the desired gains index.
The relative viabilities of homozygous and heterozygous karyotypes were measured by making crosses between strains ofD. ananassae homozygous for ST or inverted gene orders in the second and third chromosomes. The strains utilized during the present study originated from widely separated localities in India, Kuala Lumpur and Kota Kinabaru, Malaysia and Chian Mai, Thailand. The presence of heterosis in many interpopulation crosses is evident from the results which show that the inversion heterozygotes formed by chromosomes coming from distant populations exhibit heterosis. On the other hand, heterosis is absent in two intrapopulation crosses. Thus the present results provide evidence that heterozygosis for many genes and gene complexes does produce high fitness without previous selectional coadaptation.
A complete diallel cross of four broiler breeds was made to investigate whether there are breed differences in the combining abilities for the traits, body weight, weight gain and feed efficiency, measured during the growing period from 4 to 12 weeks of age. Data collected from male and female birds were analysed separately. General combining ability (GCA) was found to be the largest and most significant source of variation contributing to differences between crosses for all the traits, in both male and female birds. Specific combining ability (SCA) was important for body weight in both sexes and for weight gain in females. Feed efficiency in both sexes did not appear to be influenced by SCA effects. Reciprocal effects (RE) were generally absent in both sexes for all the traits, except possibly for feed efficiency.
Heritability estimates of five quantitative characters, namely, yield, girth, girth increment, virgin bark and renewed bark thickness, of the breeding Phase III Hevea families have been obtained by variance component analyses. In general, the combined heritability estimates for various characters were low to moderate. The heritabilities of these characters based on female variance components, however, were high, suggesting that considerable improvement of each of the characters could be achieved in properly designed experiments.Estimates of heritability for average yields (Range: 0.11-0.34) over different years showed that the first three years' yield was adequate for predicting estimates of genetic variance for the average of five years' yield.Correlation studies on yield with other characters indicated considerable influence of environment, with genetic correlations accounting for about 0.07 to 0.36 in the characters studied.Expected direct response to selection in yield and correlated response in yield to selection for girth at opening and virgin bark thickness have been calculated using three arbitrary values of selection intensity. The efficiency of the correlated response was found to be approximately half that of the direct response. However, the indirect selection for yield using virgin bark thickness appeared to be more favourable than that using the girth at opening favoured by earlier workers.
Glucose phosphate isomerase (E.C. 5.3.1.9) and phosphoglucomutase (E.C. 2.7.5.1) were found to be polymorphic in a laboratory colony of Aedes albopictus. The glucose phosphate isomerase locus is represented by two alleles resulting in three genotypes, while the phosphoglucomutase locus is represented by at least five alleles giving rise to a total of 15 genotypes. The inheritance of these two enzymes is of the Mendelian type with codominant alleles. Present data indicate that these genes are not linked.Of 105 mosquitoes analysed for these two gene-enzyme systems, the frequencies for glucose phosphate isomerase alleles are Gpi (S)=0.68 and Gpi (F)=0.32, while the frequencies for phosphoglucomutase alleles are Pgm (A)=0.16, Pgm (B)=0.11, Pgm (C)=0.19, Pgm (D)=0.30 and Pgm (F)= 0.24. The frequencies of the three glucose phosphate isomerase genotypes are in accord with Hardy-Weinberg expectations (X 1 (2) =2.74). Similarly, the frequencies of the 15 phosphoglucomutase genotypes probably do not differ significantly from Hardy-Weinberg expectations (X 10 (2) = 18.45).
Estimates of general combining ability of parents for yield and girth obtained separately from seedlings and their corresponding clonal families in Phases II and IIIA of the RRIM breeding programme are compared. A highly significant positive correlation (r = 0.71***) is found between GCA estimates from seedling and clonal families for yield in Phase IIIA, but not in Phase II (r = -0.03(NS)) nor for girth (r= -0.27(NS)) in Phase IIIA. The correlations for Phase II yield and Phase IIIA girth, however, improve when the GCA estimates based on small sample size or reversed rankings are excluded.When the best selections (based on present clonal and seedling information) are compared, all five of the parents top-ranking for yield are common in Phase IIIA but only two parents are common for yield and girth in Phases II and IIIA respectively. However, only one parent for yield in Phase II and two parents for girth in Phase IIIA would, if selected on clonal performance, have been omitted from the top ranking selections made by previous workers using seedling information.These findings, therefore, justify the choice of parents based on GCA estimates for yield obtained from seedling performance. Similar justification cannot be offered for girth, for which analysis is confounded by uninterpretable site and seasonal effects.
Seven varieties of long bean, which included three local and four exotic, were crossed in a complete diallel. This was an attempt to study the inheritance of crude protein content, protein yield, flowering date, pod yield and yield components.Both additive and non-additive gene effects were responsible for the genetic variation in the diallel population. However, dominance variance was more important than additive variance in crude protein content, number of pods per plant and number of seeds per pod. For seed weight and pod length, additive variance was more important.The crude protein content, protein yield and number of pods per plant appeared to be controlled by overdominance effects. Partial dominance seemed to be the case for flowering date, pod length and seed weight; complete to overdominance for pod yield. High protein appeared to be associated with recessive genes whereas there was a general trend of high yielding parents carrying more dominant genes.
Based on an improved C-banding technique, the C-banding patterns of all 11 diploid Aegilops species were described and compared. All diploid species exhibit characteristically different patterns which enable the chromosomes of any complement to be identified individually. These patterns confirm existing genome symbols and provide further evidence for the suggested changes in genome symbols of Ae. umbellulata and Ae. sharonensis, U and S(sh) respectively. Furthermore, Ae. uniaristata should be given a separate symbol, probably N. Aegilops speltoides and Ae. sharonensis could be possible donors to the B genome of wheat. Interspecific divergence in these diploid species has been accompanied by either amplification or deletion as well as massive repatterning of heterochromatin from the centromere to the telomere.
Four out of 10 diploid orchid species showed "complement fractionation" a complex cytological phenomenon, hitherto reported only in polyploid plants. The manifestation of this phenomenon during meiosis is the formation of chromosome subgroups resulting eventually in cells with more than the usual four sporads; five or six being the optimum number in the investigated orchid species. No implications whatsoever can be deduced as to the genetic or genomic constitution of the end products. The presence of the phenomenon in these orchid species could perhaps indicate a polyploid ancestry or concealed hybridity. The operation of "complement fractionation", however, could be interpreted as an alternative evolutionary pathway opposed to polyploidy.
Crosses were made between four varieties ('Mahsuri', 'Setanjung", 'MR84" and 'MR103") of Oryza sativa L. (2n=24, AA) and one accession of O. minuta (2n= 8, BBCC). The seed set obtained ranged between 9.5% and 25.1% depending on the rice variety used. By rescuing 14-day-old embryos and culturing them on 25%-strength MS medium we obtained a total of 414 F1 hybrids. The F1s were vigorous, tillered profusely, were perennial and male-sterile. The hybrids were triploid (ABC) with 36 chromosomes and showed irregular meiosis. The average frequency and range of chromosome associations at metaphase I or early anaphase I pollen mother cells of F1 plants were 29.31(16-36) Is +3.32(0-10) IIs+0.016(0-1) IIIs+0.002(0-1) IVs. Upon backcrossing the original triploid hybrids and colchicine-treated hybrids to their respective recurrent parents, and further embryo rescue, 17 backcross-1 (BC1) plants were obtained. Of all the crosses using MR84, no BC1 plant was obtained even after pollinating 13 894 spikelets of the triploid hybrid. The BC1s were similar in appearence to the F1s and were male-sterile, their chromosome number ranged from 44 to 48. By backcrossing these BC1s and nurturing them through embryo rescue, we obtained 32 BC2 plants. Of these, however, only 18 plants grew vigorously. One of these plants has 24 chromosomes and the other 17 have chromosome numbers ranging between 30 and 37. The 24-chromosome plant was morphologically similar to the O. sativa parent and was partially fertile with a pollen and spikelet fertility of 58.8% and 12.5% respectively. All of the F1 and BC1 plants were found to be resistant to five Malaysian isolates (XO66, XO99, XO100, XO257 and XO319) of Xanthomonas campestris pv oryzae. Amongst the BC2s, the reaction varied from resistant to moderately susceptible. The 24-chromosome BC2 plant was resistant to the four isolates and moderately resistant to isolate XO100 to which the O. sativa parent was susceptible.
KEY MESSAGE: A novel tetraploid S. spontaneum with basic chromosome x = 10 was discovered, providing us insights in the origin and evolution in Saccharum species. Sugarcane (Saccharum spp., Poaceae) is a leading crop for sugar production providing 80% of the world's sugar. However, the genetic and genomic complexities of this crop such as its high polyploidy level and highly variable chromosome numbers have significantly hindered the studies in deciphering the genomic structure and evolution of sugarcane. Here, we developed the first set of oligonucleotide (oligo)-based probes based on the S. spontaneum genome (x = 8), which can be used to simultaneously distinguish each of the 64 chromosomes of octaploid S. spontaneum SES208 (2n = 8x = 64) through fluorescence in situ hybridization (FISH). By comparative FISH assay, we confirmed the chromosomal rearrangements of S. spontaneum (x = 8) and S. officinarum (2n = 8x = 80), the main contributors of modern sugarcane cultivars. In addition, we examined a S. spontaneum accession, Np-X, with 2n = 40 chromosomes, and we found that it was a tetraploid with the unusual basic chromosome number of x = 10. Assays at the cytological and DNA levels demonstrated its close relationship with S. spontaneum with basic chromosome number x = 8 (the most common accessions in S. spontaneum), confirming its S. spontaneum identity. Population genetic structure and phylogenetic relationship analyses between Np-X and 64 S. spontaneum accessions revealed that Np-X belongs to the ancient Pan-Malaysia group, indicating a close relationship to S. spontaneum with basic chromosome number of x = 8. This finding of a tetraploid S. spontaneum with basic chromosome number of x = 10 suggested a parallel evolution path of genomes and polyploid series in S. spontaneum with different basic chromosome numbers.