Genetic Diversity Analysis of 53 Indonesian Rice Genotypes using 6K Single Nucleotide Polymorphism Markers

<p>Indonesia is rich in rice genetic resources, however, only a small number has been used in variety improvement programs. This study aimed to determine the genetic diversity of Indonesian rice varieties using 6K SNP markers. The study was conducted at ICABIOGRAD for DNA isolation and IRRI for SNP marker analysis. Genetic materials were 53 rice genotypes consisting of 49 varieties and 4 check genotypes. SNP markers used were 6K loci. Results showed that among the markers analyzed, only 4,606 SNPs (76.77%) were successfully read. The SNP markers covered all twelve rice chromosomes of 945,178.27 bp. The most common allele observed was GG, whereas the least allele was TG. Dendrograms of the 53 rice varieties analyzed with 4,606 SNPs demonstrated several small groups containing genotypic mixtures between indica and japonica rice, and no groups were found to contain firmly indica or japonica type. Structure analysis (K = 2) with value of 0.8 showed that the 53 rice varieties were divided into several groups and each group consisted of 4 japonica, 2 tropical japonica, 46 indica, and 1 aus rice type, respectively. IR64 and Ciherang proved to have an indica genome, while Rojolele has japonica one. Dupa and Hawara Bunar, usually grouped into tropical japonica rice, were classified as indica type, and Hawara Bunar has perfectly 100% indica type. The results of this study indicated that rice classification (indica-japonica) which is usually classified based only on morphological characters, e.g. grain and leaf shapes, is not enough and classification based on SNP markers should be considered for that purpose.</p>

Influence of genotypic mixtures on field pea yield and competitive ability

Darras, S., McKenzie, R. H., Olson, M. A. and Willenborg, C. J. 2015. Influence of genotypic mixtures on field pea yield and competitive ability. Can. J. Plant Sci. 95: 315–324. Field pea breeding programs have been very successful at improving plant and disease resistance; however, limited success has been achieved in improving the competitive ability of field pea. A study was conducted to determine whether growing field pea in two-way genotypic mixtures could improve the crop's yield and competitive ability. A second objective was to determine if genetic relatedness had any effect on the mixing ability of genotypes. Genotypes were chosen on the basis of pedigree and included two sister lines (CDC1987-3 and CDC1897-14), their common parent (Eclipse), and a distantly related genotype (Midas). The four genotypes were grown as pure stands and as all possible two-way mixtures in field experiments conducted at Lethbridge and St. Albert, Alberta, from 2010 to 2011. The results revealed that CDC1897-3×Eclipse suppressed the model weed (barley); it reduced seed production by 47% (442 kg ha−1) and 61% (391 kg ha−1) compared with the same components within pure stands at Lethbridge 2010 and Lethbridge 2011, respectively. The same mixture also reduced model weed (barley) biomass production by 61% (831 kg ha−1) at St. Albert in 2010, and by 41% (1372 kg ha−1) at Lethbridge in 2010. Although mixtures demonstrated the potential to improve field pea competitive ability, results were not consistent across site-years. However, some mixtures did improve yield and competitive ability over the most poorly competitive genotypes in pure stand.

Mixtures of Complete and pif1- and pif2-Deficient Genotypes Are Required for Increased Potency of an Insect Nucleopolyhedrovirus

ABSTRACT The insecticidal potency of a nucleopolyhedrovirus population (SfNIC) that infects Spodoptera frugiperda (Lepidoptera) is greater than the potency of any of the component genotypes alone. Occlusion bodies (OBs) produced in mixed infections comprising the complete genotype and a deletion genotype are as pathogenic as the natural population of genotypes from the field. To test whether this increased potency was due to the deletion or to some other characteristic of the deletion variant genome, we used the SfNIC-B genome to construct a recombinant virus (SfNIC-BΔ16K) with the same 16.4-kb deletion as that observed in SfNIC-C and another recombinant (SfNIC-BΔpifs) with a deletion encompassing two adjacent genes (pif1 and pif2) that are essential for transmission per os. Mixtures comprising SfNIC-B and SfNIC-BΔ16K in OB ratios that varied between 10:90 and 90:10 were injected into insects, and the progeny OBs were fed to larvae in an insecticidal potency assay. A densitometric analysis of PCR products indicated that SfNIC-B was generally more abundant than expected in mixtures based on the proportions of OBs used to produce the inocula. Mixtures derived from OB ratios of 10, 25, or 50% of SfNIC-BΔ16K and the corresponding SfNIC-B proportions showed a significant increase in potency compared to SfNIC-B alone. The results of potency assays with mixtures comprising various proportions of SfNIC-B plus SfNIC-BΔpifs were almost identical to the results observed with SfNIC-BΔ16K, indicating that deletion of the pif gene region was responsible for the increased potency observed in mixtures of SfNIC-B and each deletion recombinant virus. Subsequently, mixtures produced from OB ratios involving 10 or 90% of SfNIC-BΔ16K with the corresponding proportions of SfNIC-B were subjected to four rounds of per os transmission in larvae. The composition of each experimental mixture rapidly converged to a common equilibrium with a genotypic composition of ∼85% SfNIC-B plus ∼15% SfNIC-BΔ16K. Nearly identical results were observed in peroral-passage experiments involving mixtures of SfNIC-B plus SfNIC-BΔpifs. We conclude that (i) the deletion of the pif1 and pif2 region is necessary and sufficient to explain the increased potency observed in mixtures of complete and deletion genotypes and (ii) viral populations with decreased ratios of pif1- and pif2-deficient genotypes in the virus population increase the potency of genotypic mixtures and are likely to positively influence the transmission of this pathogen.

AFLP fingerprinting reveals pattern differences between template DNA extracted from different plant organs

AFLP (amplified fragment length polymorphism) fingerprinting of cultivars of bread wheat (Triticum aestivum) and some of its wild relatives has allowed the efficient detection of large numbers of polymorphic amplified fragments. While the reproducibility of fingerprints in repeated experiments is high, pattern differences were observed between fingerprints obtained from seed and leaf DNA template from the same wheat accession. These distinct organ specific amplified DNA fragments were shown to be due neither to genotypic mixtures nor to pathogen contamination. They are likely a result of differences in DNA methylation between organs. Even greater numbers of organ specific amplified fragments were observed when fingerprints obtained from the root and shoot of individual seedlings of the wheat relatives Aegilops mutica and Aegilops speltoides were compared. This phenomenon underlines the importance of ensuring that DNA is extracted from physiologically uniform tissue in phylogenetic studies based on AFLP fingerprints. For this purpose, mature seed is a convenient source.Key words: AFLPs, fingerprinting, genome mapping, organ specificity.

BREEDING STRATEGIES FOR DEVELOPING DRY BEAN CULTIVARS RESISTANT TO BRUCHID WEEVILS

The presence of arcelin protein in the seeds of common bean, Phaseolus vulgaris L., provides resistance to the Mexican bean weevil and to a lesser degree, the common bean weevil. Fast, accurate identification of single seeds containing arcelin facilitates the transfer of alleles for each of four different arcelin types through standard crossing procedures. Seed yields and other traits of near-isogenic lines that contain different alleles were comparable to the standard parent, Porrillo 70. Genotypic mixtures containing resistant and susceptible seeds produced seed yields comparable to Porrillo 70, which suggests that heterogeneous populations offer the potential for stable resistant cultivars.

Specificity of association between Bacillus isolates and genotypes of Lolium perenne and Trifolium repens from a grass – legume pasture

Specificity between plants and associated rhizosphere bacteria was investigated using species and genotypic mixtures of Lolium perenne L. (perennial ryegrass) and Trifolium repens L. (white clover) inoculated with Bacillus strains isolated from rhizosphere soil of the pasture plants. The genotypic identity of plants was controlled by using stolon tips (Trifolium) and tillers (Lolium) of three genotypes of each species collected from a 45-year-old permanent pasture. Inoculation of plants in the greenhouse with Bacillus isolates that had coexisted in the field with the Lolium component of a Lolium–Trifolium mixture increased Lolium root and shoot weight. Root and nodule weight of Trifolium in mixture regardless of its genotype was also higher when coexistent Bacillus–Lolium combinations were present. The presence of other coexistent Bacillus–plant or plant–plant combinations did not enhance performance of either pasture species. The identity of the Rhizobium leguminosarum biovar trifolii strains that formed Trifolium root nodules was unaffected by inoculation with Bacillus. Key words: Trifolium repens, Lolium perenne, Bacillus, specificity, rhizosphere, yield.