The wild ancestry of maize has long been a puzzle. Maize shows extraordinary phenotypic and genetic diversity with no obvious morphological similarity to any of its wild relatives. Beadle’s teosinte hypothesis, which regards teosinte as the sole wild ancestor of maize, has become widely accepted as the most probable model of maize evolution based on taxonomic, genetic, and other types of evidence. Molecular studies have refined the teosinte hypothesis by identifying a particular form of teosinte, Zea mays ssp. parviglumis, as the direct ancestor of maize. Maize and teosinte therefore provide a typical case in which modern molecular genetic analyses, in the absence of obvious morphological similarity, have been critical for distinguishing the exact ancestor of a crop from other close wild relatives. Furthermore, a recent microsatellite-based study shows that all extant pre-Columbian maize landraces arose from Z. mays ssp. parviglumis roughly 9,000 years ago through a single domestication event in the central Balsas River drainage (southern Mexico). That model, showing that maize is a domesticated form of Z. mays ssp. parviglumis, provides a logical, practical framework for investigations of the genetic mechanisms that drove maize domestication and diversification. This points up the importance of knowing exact origins in studies that use crops and their wild relatives as models. An overview of the progress in genetic and evolutionary studies is presented herein to clarify the identity of the wild progenitor of maize. Implications of recent findings on the origin of maize diversity are discussed.
A Sri Lankan indica rice (Oryza sativa L.) cultivar Rathu Heenati was found to be resistant to all the four biotypes of the brown planthopper (BPH) (Nilaparvata lugens Stål). In the present study, we constructed a linkage map to identify the locus (loci) for the BPH resistance genes, using an F2 population from a cross between Rathu Heenati and a susceptible cultivar 02428. Insect resistance was evaluated using 156 F2:3 lines and the genotype of each F2 plant was inferred from the phenotype of the corresponding F2:3 lines. Three loci detected by QTL (quantitative trait locus) analysis, were assigned to chromosomes 3, 4 and 10. The phenotypic variance of the three QTLs indicated that the QTL on chromosome 4 is a major BPH resistance gene in Rathu Heenati. Through linkage analysis, it was found that this BPH resistance gene was located between two SSR markers RM8213 and RM5953 on the short arm of chromosome 4, with map distances of 3.6 cM and 3.2 cM, respectively. This gene, tentatively designated as Bph17, should be useful for the breeding of varieties resistant to BPH in a marker-assisted selection (MAS) program.
The effectiveness of marker-based selection (MBS) for enhancing the efficiency of two conventional breeding methods of self-fertilizing crop plants, i.e., generation-accelerated bulk breeding (GAB) and doubled haploid breeding (DHB), is evaluated. When incorporated into GAB, MBS is assumed to be applied in F2 and F3 generations based on DNA markers that are linked with desirable trait genes. The effectiveness of MBS is evaluated based on its contribution to increasing the probability of obtaining the desired genotype. Our calculations of the probability show that the effectiveness of MBS depends on the number of trait genes involved in the breeding objective as well as the number of available markers; MBS will produce a great increase in the probability when more than about 12 genes are involved in the breeding objective and markers are available for several or more of these trait genes. In such a case, MBS is useful even when as few as 100 plants are tested in F2 and F3 generations, compared to conventional GAB in which 2000 plants are grown for generation acceleration. The effectiveness of MBS increases in the presence of repulsion linkage between desirable trait genes, whereas it decreases in the presence of coupling linkage. Although codominant markers are superior under most practically possible conditions, dominant markers (linked with desirable trait genes) could be superior when relatively few, roughly fewer than 12, genes are involved in the breeding objective and desirable trait genes are linked prevalently in the coupling phase. When MBS is based on more than several codominant markers, it is important to widen the range of the marker genotypes to be selected; not only the best but also the second and third best, partially heterozygous genotypes should be selected. Linkage between trait genes and markers needs not to be perfect; when many markers are available, the advantage of MBS is not lost even with a map distance as long as 10 cM. When desirable trait genes are linked prevalently in the repulsion phase, MBS could effectively be combined with DHB for eliminating unpromising doubled haploid genotypes prior to field test, or for selecting from an F2 population, plants that should be treated for doubled haploidization.
The authors report here a case of hybrid sterility between an indica cultivar, IR36 and a weedy strain, Ludao, which naturally grows in and around farms in Jiangsu province, China. A genome-wide analysis was performed with a backcross population of IR36/Ludao//IR36 using a total of 151 simple sequence repeat (SSR) markers covering the entire rice linkage map. As a result, two loci were found to induce independently the hybrid sterility via female gamete abortion. Of the two loci, the locus on chromosome 6 corresponded to S10 according to its chromosomal location, while the other one on chromosome 7 was different from all the previously reported hybrid sterility loci, and was designated as S30(t). Based on the allelic interaction which causes female gamete abortion, two alleles were identified: S30(t)-i in IR36 and S30(t)-j in Ludao. In the heterozygote, S30(t)-i/S30(t)-j, which was semi-sterile, female gametes carrying S30(t)-j were partially aborted. A javanica variety, Ketan Nangka, and an Aus variety, N22, carried the neutral allele, S30(t)-n. Thus, Ludao was found to harbor a hybrid sterility gene different from that of existing cultivars in China, as an evidence of its origin from an ancient wild rice variety.
Genetic variation among flowering cherries (Prunus subgenus Cerasus) was characterized by SSR markers developed from peach, sweet cherry and sour cherry, using a total of 144 individuals from 15 taxa. Twenty-five out of 85 SSR markers showed amplification in all tested samples, indicating that 29% of SSRs developed from related species could be transferred to flowering cherries. In contrast, 25 SSRs gave no amplification for any tested samples. The mean number of alleles per locus and the mean number of ne (the effective number of alleles per locus) assessed by 9 transferable SSRs were 17.3 and 7.3, respectively. All but 2 individuals were distinguished by 9 SSR loci. Genetic variation among flowering cherries was higher than that in peach and sweet cherry cultivars. On the other hand, the mean number of alleles per locus on each taxon ranged from 1.9 to 7.7, suggesting that each taxon accounted for a rather small part of the variation of flowering cherries. A phenogram of 144 individuals and a phenogram of 14 taxa based on SSR analysis were constructed. Many taxa were clustered in the sections to which they belong. Four taxa of section Incisae were closely related. Two taxa of section Apetalae were also closely related. P. maximowiczii and P. pendula f. ascendens were distant from the other Japanese taxa. These results were in good accordance with the morphological classification. We found the SSR markers developed from related species useful for evaluating the genetic variation and clustering flowering cherries.
In cultivated rice Oryza sativa, although physiological and molecular biological studies have demonstrated the existence of a high intra-species diversity, there are few reports related to the molecular cytological diversity. To examine the molecular cytological diversity in O. sativa, a tandem repeat-sequence Os48 was visualized using fluorescence in situ hybridization (FISH) in various rice varieties. Diversity was reflected by differences in the number of FISH signals. The number of loci detected was almost the same among the O. sativa subspecies japonica varieties, but differed significantly among the O. sativa subspecies indica varieties. The difference in the number of Os48 loci reflected differences in the chromosomal structure. In O. sativa, repeat sequences of 45S rDNA were also mapped to distal region(s) of the chromosome(s). Two-colored FISH of rDNA and Os48 revealed a common chromosomal structure within japonica varieties and indica varieties, but a distinctly different structure between japonica and indica varieties. The present study indicated that there was less cytological diversity among japonica varieties than among indica varieties. FISH results also allowed considerations of the domestication of cultivated rice O. sativa.
A rice diversity research set of germplasm (RDRS) was developed based on a genome-wide RFLP polymorphism survey of 332 accessions of cultivated rice (Oryza sativa L.). The accessions used in the initial survey were selected based on the passport data from the whole collection maintained at the Genebank of the National Institute of Agrobiological Sciences (NIAS). These accessions were analyzed using 179 nuclear RFLP markers. A total of 554 alleles were detected, and the number of alleles per locus ranged from 2 to 8 (mean 3.1). Principal coordinate analysis using RFLP data enabled to classify the accessions into three major groups, one Japonica and other two Indica. To develop a rice diversity research set of germplasm, the RFLP data on the 332 accessions were subjected to cluster analysis and 67 groups were recognized at a similarity index of 0.915. A single accession from each of the 67 groups was selected. These 67 accessions retained 91% of the alleles detected in the original 332 accessions, and covered the variation of the initial set of accessions in terms of several agro-morphological traits. The 69 accessions including varieties from 19 countries and the reference varieties, Nipponbare and Kasalath, were selected for the development of a rice diversity research set of germplasm. This collection which is presently well characterized at the molecular level will be used for the detailed genetic studies and rice improvement.
Fifty-four accessions of local soybean strains collected from villages in the western part of the Shikoku Mountains were examined to assess genetic variation using the RAPD method. The accessions included 25 yellow, 17 black, 2 brown and 10 green seed-coat strains. Sixty-eight out of 138 bands detected by 21 RAPD primers were polymorphic. The average genetic distance for all the pairwise combinations was 0.114 ± 0.0336, which indicates that the local strains retained more than 80% of the genetic variation of the Japanese landraces reported previously. The genetic distance within yellow strains, black strains (including two brown strains) and green strains was 0.114 ± 0.0273, 0.0969 ± 0.0333 and 0.0840 ± 0.0309, respectively. These values were significantly different from each other. The genetic distance between the strains in groups with different seed-coat colors was significantly different from zero. The coefficient of genetic differentiation, GST, among the seed-coat colors was 0.174, indicating a large genetic differentiation. The NJ tree revealed the presence of three clusters: two were mainly composed of yellow and black strains, respectively, and the other one consisted of a mixture of yellow, black and green strains. However, monophyly of the seed-coat color groups was not supported except for some small subgroups. These results suggest that repeated introduction of seeds from outside seed sources and/or frequent hybridization among the strains with different seed-coat colors within the region had occurred during the long history of soybean cultivation in the Shikoku Mountains.
To identify the region related to the protein transport of mitochondrial uncoupling protein (UCP), we divided wheat UCP (WhUCP1b) protein into three regions (D1, D2 and D3) and fused them with green fluorescent protein (GFP) as an N-terminal signal peptide. Four fusion proteins (WhUCP::GFP, D#::GFP) were expressed in yeast cells to observe the transport of the fusion proteins to mitochondria in vivo. The mitochondrial localization of the four fusion proteins was visualized using GFP fluorescence as a reporter. Western blot analysis also revealed that all four fusion proteins were transported to the mitochondria. The D2 region had the highest protein transport efficiency, and the D1 and D3 regions also had some protein transport activity. Another kind of fusion protein constructed using the D2 region as an internal signal peptide (DSR::D2::GFP) was also successfully targeted to mitochondria. These results demonstrate that the D2 region of WhUCP1b possesses the highest activity directing protein transport to the mitochondria among three regions, and that the protein transport activity of the D2 region is independent on its position within the fusion protein.
The cDNA clone of the sweetpotato isoamylase gene, encoding starch-debranching enzyme (IbIsa1) in sweetpotato (Ipomoea batatas (L.), cv. Kokei 14), was isolated and sequenced. The amino acid sequence of IbIsa1 is 70% and 79% identical to that of AtIsa1 from Arabidopsis and StIsa1 from potato, respectively. DNA gel-blot analysis demonstrated that at least two copies IbIsa1 are present in the sweetpotato genome. IbIsa1 was found to be strongly expressed in tuberous root. The transcript level of IbIsa1 in the root of rooted single-leaf cuttings was extremely low during the first 15 to 40 days after planting. The transcript levels continuously increased up to 50 days, at which time the tuberous root was almost completely developed. This indicates that IbIsa1 may work in concert with AGPase large subunit, GBSSI and SBEII during the primary phase of starch granule formation.
Allelic variation of high molecular weight glutenin subunits (HMW-GS) encoded by Glu-A1, Glu-B1 and Glu-D1 in wheat landraces originating from the Xinjiang Uygur Autonomous District (Xinjiang District) of China was investigated by SDS-PAGE and the relationship between the variation and the winter habit was examined. The most frequent allele at the Glu-A1 locus was Glu-A1c (null allele: 75.5%), followed by Glu-A1b encoding subunit 2* (22.3%). These two alleles were distinctive at Glu-A1 in the landraces of both spring and winter cultivars. No difference in allele frequency was found between the spring and the winter wheat cultivars. At the Glu-B1 locus, the most frequent allele was Glu-B1b (90.8%) encoding subunits 7 + 8, the allele frequency of which was almost the same between the spring and the winter wheat cultivars. Glu-D1a (72.0%) encoding subunits 2 + 12 was a major allele at the Glu-D1 locus among the landraces. Although no cultivar with Glu-d1f encoding subunits 2.2 + 12 was found, the novel subunit pair 2.6 + 12 (24.5%) was observed only in the winter wheat cultivars. Subunit 2.6 was slightly less mobile than subunit 2.2. The major Glu-D1 allele was Glu-D1a (94.5%) among the spring wheat cultivars and this allele characterized the spring wheat cultivars in the Xinjiang District. Both the subunit pair 2.6 + 12 encoded by the Glu-D1bp(t) allele (58.5%) and the subunit pair 2 + 12 encoded by the Glu-D1a allele (40.7%) predominated among the winter wheat cultivars. The large difference in allelic variation at the Glu-D1 locus suggested that the origin of the spring wheat cultivars was different from that of the winter wheat cultivars. The absence of landrace with Glu-D1f suggested that Xinjiang wheat was not related to Japanese wheat.