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To unravel the plastid genome diversity among the cultivated groups of the pigeonpea germplasm, we characterized the SNP occurrence and distribution of 142 pigeonpea mini-core collections based on their reference-based assembly of the chloroplast genome. A total of 8921 SNPs were found, which were again filtered and finally 3871 non-synonymous SNPs were detected and used for diversity estimates. These 3871 SNPs were classified into 12 groups and were present in only 44 of the 125 genes, demonstrating the presence of a precise mechanism for maintaining the whole chloroplast genome throughout evolution. The Acetyl-CoA carboxylase D gene possesses the maximum number of SNPs (12.29%), but the Adenosine Tri-Phosphate synthatase cluster genes (atpA, atpB, atpE, atpF, atpH, and atpI) altogether bear 43.34% of the SNPs making them most diverse. Various diversity estimates, such as the number of effective alleles (1.013), Watterson's estimate (0.19), Tajima's D (– 3.15), Shannon's information index (0.036), suggest the presence of less diversity in the cultivated gene pool of chloroplast genomes. The genetic relatedness estimates based on pairwise correlations were also in congruence with these diversity descriptors and indicate the prevalence of rare alleles in the accessions. Interestingly, no stratification was observed either through STRUCTURE, PCoA, or phylogenetic analysis, indicating the common origin of the chloroplast in all the accessions used, irrespective of their geographical distribution. Further 6194 Cleaved Amplified Polymorphic Sequences (CAPS) markers for 531 SNPs were developed and validated in a selected set of germplasm. Based on these results, we inferred that all of the cultivated gene pools of pigeonpea have a common origin for the chloroplast genome and they possess less diversity in protein-coding regions, indicating a stable and evolved plastid genome. At the same time, all diversity analysis indicates the occurrence of rare alleles, suggesting the suitability of the mini-core collection in future pigeonpea improvement programs. In addition, the development of chloroplast genome-based CAPS markers would have utility in pigeonpea breeding programs. [ABSTRACT FROM AUTHOR]

Cleaved Amplified Polymorphic Sequences (CAPS) markers are applicable in a wide range of tasksin plant biology. They have been developed for plant genetics and breeding and become especially useful. This mini-review analyzes information about the application of CAPS markers within the past3–5 years. In the presented study, special attention is focused on CAPS markers linked with genes controlling important agricultural traits in different crops. The main principles of the developmentand analysis of CAPS markers, as well as advantages and disadvantages of this type of molecular markers, are briefly outlined in the beginning of this review. CAPS markers are based on PCR amplification of DNA fragments with specific primers followed by digestion with restriction enzymes and separation of the products in agarose gel. Functional CAPS markers can be developed on the known sequence of a gene of interest for the analyses of its structure, function, expression, and regulation. CAPS closely linked to the gene of interest are especially helpful for Marker-Assisted Selection, and they are widely used in the breeding of wheat, barley, soybean, potato, tomato, and other crops for tolerance to various pathogens. CAPS markers are often used for the preparation of genetic maps and fine mapping of studied genes. For some plants, first moleculargenetic maps were prepared using CAPS. This method was also successfully used for the mapping of both individual genes and QTLs controlling such important traits as plant growth habit, grain quality, and tolerance to pathogens in cereals, as well as the shape of tomato fruit. CAPS have important applications in the analyses of genetic polymorphism and phylogeny, particularly, in closely related species. Thus, CAPS are an effective tool for molecular-genetic research and plant breeding.

Cleaved Amplified Polymorphic Sequences (CAPS) markers are applicable in a wide range of tasks in plant biology. They were developed recently for plant genetics and breeding and have become especially useful. This mini-review contains an analysis of the information on the application of CAPS markers from the past 3-5 years. In the study presented, special attention was focused on CAPS markers linked with genes controlling important agricultural traits in different crops. The main principles of the development and analysis of CAPS markers as well as advantages and disadvantages of this type of molecular markers are briefly addressed in the beginning of this review. CAPS markers are based on PCR-amplifications of DNA fragments with specific primers, after the digestion of restriction enzymes and separation of the products in an agarose gel. Functional CAPS markers can be developed on the known sequence of a Gene of Interest for the analysis of its structure, function, expression and regulation. CAPS closely linked to the Gene of Interest are especially helpful for Marker-Assisted Selection, and they are widely used in the breeding of wheat, barley, soybean, potato, tomato and other crops for the tolerance to various pathogens. CAPS markers are often used for the preparation of genetic maps and fine mapping of studied genes. Molecular-genetic maps were prepared for some plants using CAPS. This method was also successfully used for the mapping of both individual genes and QTLs controlling such important traits as plant development, grain quality and tolerance to pathogens in cereals, as well as shape of tomato fruit. CAPS have important applications in the analyses of genetic polymorphism and phylogeny, especially in closely related species. Thus CAPS can be used as an effective tool for molecular-genetic study and plant breeding. [ABSTRACT FROM AUTHOR]

Bemisia tabaci Gennadius biotypes B and Q are two of the most important worldwide agricultural insect pests. Genomic sequences of Type-2 B. tabaci chemosensory protein (BtabCSP2) were cloned and sequenced in B and Q biotypes, revealing key biotype-specific variations in the intron sequence. A Q260 sequence was found specifically in Q-BtabCSP2 and Cucumis melo LN692399, suggesting ancestral horizontal transfer of gene between the insect and the plant through bacteria. A cleaved amplified polymorphic sequences (CAPS) method was then developed to differentiate B and Q based on the sequence variation in exon of BtabCSP2 gene. The performances of CSP2-based CAPS for whitefly recognition were assessed using B. tabaci field collections from Shandong Province (P.R. China). Our SacII based CAPS method led to the same result compared to mitochondrial cytochrome oxidase-based CAPS method in the field collections. We therefore propose an explanation for CSP origin and a new rapid simple molecular method based on genomic DNA and chemosensory gene to differentiate accurately the B and Q whiteflies of the Bemisia complex around the world. [ABSTRACT FROM AUTHOR]

We developed 708 gene-based markers for citrus genome analysis. Sequence-tagged site (STS) primers were designed that were located in conserved exon regions and whose PCR products spanned genomic introns. Of these, 79.7 % comprised cleaved amplified polymorphic sequence markers. The gene-based markers and their annotation and position on Clementine scaffolds ver. 1.0 permitted comparison of the genetic map and the Clementine genome sequence. The 708 gene-based markers were used to construct a genetic map using the 87 progenies (AG population) from the cross between 'Okitsu 46 gou' ('Sweet Spring' ('Ueda unshiu' ( Citrus unshiu) × Hassaku ( Citrus hassaku Hort. ex Tanaka)) × 'Trovita' orange) × 'Kankitsu Chukanbohon Nou 5 gou' ('Lee' ( Citrus clementina × tangelo) × Citrus kinokuni). The markers were integrated using common STSs on different phase maps in cross-pollination mode. The integrated map (AGI map) comprised 706 loci, including two morphological traits, and spanned 990.9 centimorgans (cM) with an average marker distance of 1.40 cM. These markers formed nine linkage groups (LGs) (corresponding to citrus physical chromosomes): LG-01 to LG-09 corresponded to Scaffold_01, Scaffold_07, Scaffold_09, Scaffold_06, Scaffold_03, Scaffold_02, Scaffold_04, Scaffold_08, and Scaffold_05, respectively. LG-08 and LG-09 contained morphological traits controlling embryo color and seedlessness. Eighty-eight loci comprised three or more alleles on the AGI map; 36.4 % of them were related to transcription factors and DNA-binding proteins. The 708 gene-based markers and the AGI map are valuable for integrating various citrus genetic maps, alignment of genomic sequences, chromosome assignment, and understanding the diversity of citrus germplasms. [ABSTRACT FROM AUTHOR]

The inheritance of the reaction of sunflower to downy mildew was investigated using resistant and susceptible near isogenic lines (NILs) and their F3 families. Resistance to race 730 was evaluated using the whole seedling inoculation technique. Seventy-three F3 families were inoculated, among which 54 families were resistant and 19 susceptible, fitting a 3 : 1 segregation ratio. F3 families were also studied using several PCR markers. Ten markers at the Pl6 locus, specific for the resistant line, also segregated in F3 families with a 3 : 1 ratio. The same segregation ratio occurred for microsatellite haplotypes that resembled the resistant parent, and were amplified with ORS 166 and ORS 1043. The only common fragment that was observed between resistant and susceptible parental lines was one of the TIR-NBS-LRR resistance gene analogue markers, having a restriction site. Two co-dominant cleaved amplified polymorphic sequence (CAPS) markers were obtained. The mapping data indicate that several dominant markers and two CAPS markers, developed here, completely co-segregate with the Pl6 gene conferring resistance to race 730. CAPS markers will facilitate efficient marker-assisted selection for sunflower resistance to downy mildew race 730. [ABSTRACT FROM AUTHOR]

A sample of American wild rice and other accessions of the genus Oryza were studied at polymorphic regions of nuclear, mitochondrial, and chloroplastic genomes. First, flow cytometry, genome-specific RAPD markers, and chromosome counting were utilized to verify the original ploidy and classification of 230 accessions studied. Based on these methods, 8% of the accessions were considered to be misclassified either taxonomically or as a result of contamination. Second, a fine resolution analysis was conducted at genomic regions sampled at random by RAPD markers and at specific sites of the chloroplast and mitochondrial DNA by cleaved amplified polymorphic sequence (CAPS) analysis. Phylogenetic trees resulting from phenetic and cladistic analyses of RAPD, cpDNA, and mtDNA polymorphisms were obtained. The results indicated that the American diploid species O. glumaepatula should be considered an individual species, distinct from O. rufipogon, and confirmed that the American tetraploid species (O. alta, O. grandiglumis, and O. latifolia) belong to the O. officinalis complex. The data indicate that these species should still be treated as a group rather than as three distinct species and that their closest relative is a CC-genome species. It was estimated that the diploid and tetraploid American species diverged from O. sativa – O. nivara (AA genome) and CC- and BBCC-genome species, respectively, 20 million years ago.Key words: RAPD, cleaved amplified polymorphic sequences, flow cytometry, Oryza glumaepatula, rice evolution.Des échantillons de riz sauvage américain et d'autres accessions du genre Oryza ont été étudiés au niveau de régions d'ADN polymorphes au sein des génomes nucléaire, mitochondrial et chloroplastique. D'abord, de la cytométrie en flux, des marqueurs RAPD spécifiques d'un génome et des décomptes chromosomiques ont été utilisés pour vérifier le niveau de ploïdie original et la classification des 230 accessions étudiées. Sur la base de ces travaux, 8 % des accessions se sont avérées incorrectement classifiées sur le plan taxonomique ou encore souffraient de contaminations. Ensuite, une analyse à résolution fine a été réalisée sur des régions génomiques échantillonnées au hasard à l'aide de marqueurs RAPD de même que sur des régions spécifiques de l'ADN chloroplastique ou mitochondrial grâce à des marqueurs CAPS (« cleaved amplified polymorphic sequence »). Des arbres phylogénétiques, résultant d'analyses phénétiques et cladistiques sur les polymorphismes RAPD, ADNcp et ADNmt, ont été obtenus. Les résultats indiquent que l'espèce diploïde américaine O. glumaepatula devrait être considérée comme une espèce à part, distincte de l'O. rufipogon. Il a été confirmé que les espèces américaines tétraploïdes (O. alta, O. grandiglumis et O. latifolia) appartiennent au complexe O. officinalis. Les données suggèrent que ces trois espèces devraient être traitées comme un groupe plutôt qu'en tant qu'espèces distinctes et que leur plus proche parent est une espèce à génome CC. Il a été estimé que les espèces américaines diploïdes et tétraploïdes ont divergé de l'O. sativa – O. nivara et des espèces à génome CC/BBCC il y a 20 millions d'années.Mots clés : RAPD, CAPS, cytométrie en flux, Oryza glumaepatula, évolution du riz.[Traduit par la Rédaction] [ABSTRACT FROM AUTHOR]

Molecular genetic maps were commonly constructed by analyzing the segregation of restriction fragment length polymorphisms (RFLPs). Here we described methodology-marker sequences in a new mapping based on recent documents. With the methods they were unique sequences detected by the polymerase chain reaction (PCR). Each of the methods had its limitations and the current trend was to integrate the maps produced by the different methods. Market sequences contained mainly expressed sequence tags (ESTs), polymorphic sequence-tagged sites (STSs), randomly amplified polymorphic DNA (RAPDs), cleaved amplified polymorphic sequences (CAPS), amplified fragment length polymorphism (AFLPs), genome sequence sampling (GSS) and sequence-tagged connectors (STCs) in this paper. [ABSTRACT FROM AUTHOR]