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PubMed2006

Complete assignment of the chromosomes of Gossypium hirsutum L. by translocation and fluorescence in situ hybridization mapping.

Significant progress has been made in the construction of genetic maps in the tetraploid cotton Gossypium hirsutum. However, six linkage groups (LGs) have still not been assigned to specific chromosomes, which is a hindrance for integrated genetic map construction. In the present research, specific bacterial artificial chromosome (BAC) clones constructed in G. hirsutum acc. TM-1 for these six LGs were identified by screening the BAC library using linkage group-specific simple-sequence repeats markers. These BAC clones were hybridized to ten translocation heterozygotes of G. hirsutum. L as BAC-fluorescence in situ hybridization probes, which allowed us to assign these six LGs A01, A02, A03, D02, D03, and D08 to chromosomes 13, 8, 11, 21, 24, and 19, respectively. Therefore, the 13 homeologous chromosome pairs have been established, and we have proposed a new chromosome nomenclature for tetraploid cotton.

Chromosome Mapping↗

PubMed2006

Molecular mapping of a nuclear male-sterility gene in sunflower (Helianthus annuus L.) using TRAP and SSR markers.

A nuclear male-sterile mutant, NMS 360, induced by streptomycin from an inbred maintainer line HA 89, possesses a single recessive gene, ms9, controlling male sterility. The present study identified DNA markers linked to the ms9 gene in an F2 population derived from the cross of NMS 360 x RHA 271 and maps the ms9 gene to an existing sunflower SSR linkage map. Bulked segregant analysis was performed using the target region amplification polymorphism (TRAP) marker technique and the simple sequence repeats (SSR) technique. From 444 primer combinations, six TRAP markers linked with the ms9 gene were amplified. Two markers, Ts4p03-202 and Tt3p09-529, cosegregated with the ms9 gene. The other four markers, To3d14-310, Tt3p17-390, Ts4p23-300, and Tt3p09-531, linked with ms9 at a distance of 1.2, 3.7, 10.3, and 22.3 cM, respectively. Thirty SSR primers from 17 linkage groups of a PHA x PHB cultivated sunflower linkage map were screened among the two parents and the F2 population. SSR primer ORS 705 of linkage group 10 was tightly linked to ms9 at a distance of 1.2 cM. The ms9 gene was subsequently mapped to linkage group 10 of the public sunflower SSR linkage map. The markers that were tightly linked with the ms9 gene will be useful in marker-assisted selection of male-sterile plants among segregating populations, and will facilitate the isolation of the ms9 gene by map-based cloning.

Base Sequence↗

PubMed2006

Grouping of accessions of Mexican races of maize revisited with SSR markers.

Mexican races of maize (Zea mays L.) represent a valuable genetic resource for breeding and genetic surveys. We applied simple sequence repeat (SSR) markers to characterize 25 accessions of races of maize from Mexico. Our objectives were to (1) study the molecular genetic diversity within and among these accessions and (2) examine their relationships as assumed previously on the basis of morphological data. A total of 497 individuals were fingerprinted with 25 SSR markers. We observed a high total number of alleles (7.84 alleles per locus) and total gene diversity (0.61), confirming the broad genetic base of the maize races from Mexico. In addition, the accessions were grouped into distinct racial complexes on the basis of a model-based clustering approach. The principal coordinate analyses of the four Modern Incipient hybrids corroborated the proposed parental races of Chalqueño, Cónico Norteño, Celaya, and Bolita on the basis of the morphological data. Consequently, for some of the accessions, hybridizations provide a clue that can further be used to explain the associations among the Mexican races of maize.

Alleles↗

PubMed2006

Genetic mapping and BAC assignment of EST-derived SSR markers shows non-uniform distribution of genes in the barley genome.

A set of 111,090 barley expressed sequence tags (ESTs) was searched for the presence of microsatellite motifs [simple sequence repeat (SSRs)] and yielded 2,823 non-redundant SSR-containing ESTs (SSR-ESTs). From this, a set of 754 primer pairs was designed of which 525 primer pairs yielded an amplicon and as a result, 185 EST-derived microsatellite loci (EST-SSRs) were placed onto a genetic map of barley. The markers show a uniform distribution along all seven linkage groups ranging from 21 (7H) to 35 (3H) markers. Polymorphism information content values ranged from of 0.24 to 0.78 (average 0.48). To further investigate the physical distribution of the EST-SSRs in the barley genome, a bacterial artificial chromosomes (BAC) library was screened. Out of 129 markers tested, BAC addresses were obtained for 127 EST-SSR markers. Twenty-seven BACs, forming eight contigs, were hit by two or three EST-SSRs each. This unexpectedly high incidence of EST-SSRs physically linked at the sub-megabase level provides additional evidence of an uneven distribution of genes and the segmentation of the barley genome in gene-rich and gene-poor regions.

Chromosomes, Artificial, Bacterial↗

PubMed2006

Marker-assisted characterization of Asian wheat lines for resistance to Fusarium head blight.

The major quantitative trait locus (QTL) on 3BS from Sumai 3 and its derivatives has been used as a major source of resistance to Fusarium head blight (FHB) worldwide, but resistance genes from other sources are necessary to avoid complete dependence on a single source of resistance. Fifty-nine Asian wheat landraces and cultivars differing in the levels of FHB resistance were evaluated for type II FHB resistance and for genetic diversity on the basis of amplified fragment length polymorphism (AFLP) and simple sequence repeats (SSRs). Genetic relationships among these wheat accessions estimated by cluster analysis of molecular marker data were consistent with their geographic distribution and pedigrees. Chinese resistant landraces had broader genetic diversity than that of accessions from southwestern Japan. The haplotype pattern of the SSR markers that linked to FHB resistance quantitative trait loci (QTLs) on chromosomes 3BS, 5AS and 6BS of Sumai 3 suggested that only a few lines derived from Sumai 3 may carry all the putative QTLs from Sumai 3. About half of the accessions might have one or two FHB resistance QTLs from Sumai 3. Some accessions with a high level of resistance, may carry different FHB resistance loci or alleles from those in Sumai 3, and are worth further investigation. SSR data also clearly suggested that FHB resistance QTLs on 3BS, 5AS, and 6BS of Sumai 3 were derived from Chinese landrace Taiwan Xiaomai.

Alleles↗

PubMed2006

A region of maize chromosome 2 affects response to downy mildew pathogens.

Quantitative trait loci (QTLs) for downy mildew resistance in maize were identified based on co-segregation with linked restriction fragment length polymorphisms or simple sequence repeats in 220 F2 progeny from a cross between susceptible and resistant parents. Disease response was assessed on F3 families in nurseries in Egypt, Thailand, and South Texas and after inoculation in a controlled greenhouse test. Heritability of the disease reaction was high (around 93% in Thailand). One hundred and thirty polymorphic markers were assigned to the ten chromosomes of maize with LOD scores exceeding 4.9 and covering about 1,265 cM with an average interval length between markers of 9.5 cM. About 90% of the genome is located within 10 cM of the nearest marker. Three putative QTLs were detected in association with resistance to downy mildew in different environments using composite interval mapping. Despite environmental and symptom differences, one locus on chromosome 2 had a major effect and explained up to 70% of the phenotypic variation in Thailand where disease pressure was the highest. The other two QTLs on chromosome 3 and chromosome 9 had minor effects; each explained no more than 4% of the phenotypic variation. The three QTLs appeared to have additive effects on resistance, identifying one major gene and two minor genes that contribute to downy mildew resistance.

Chromosomes, Plant↗

PubMed2006

Inheritance and mapping of a powdery mildew resistance gene introgressed from Avena macrostachya in cultivated oat.

The powdery mildew resistance from Avena macrostachya was successfully introgressed into hexaploid oat (A. sativa). Genetic analysis of F(1), F(2), F(3) and BC(1) populations from two powdery-mildew resistant introgression lines revealed that the resistance is controlled by a dominant gene, tentatively designated Eg-5. Molecular marker analysis was conducted using bulked-segregant analysis in two segregating F(3) populations. One codominant simple sequence repeats (SSR) marker AM102 and four AFLP-derived PCR-based markers were successfully developed. The SSR marker AM102 and the STS marker ASE41M56 were linked to the gene Eg-5, with genetic distances of 2 and 0.4 cM, respectively, in both mapping populations. Three STS markers (ASE45M56, ASE41M61, ASE36M55) co-segregated with Eg-5 in one population while two (ASE45M56, ASE36M55) of them linked to Eg-5 with a genetic distance of 1 cM in another population. The gene was further mapped to be in a region corresponding to linkage group 22_44+18 in the Kanota x Ogle (KO) hexaploid oat map by comparative mapping. To our knowledge, this is the first report of mapping powdery-mildew resistance in hexaploid oat. The new resistance source of A. macrostachya, together with the tightly linked markers identified here, could be beneficial in oat breeding programmes.

Ascomycota↗

PubMed2006

Molecular mapping of a recessive gene for resistance to stripe rust in barley.

Barley stripe rust, caused by Puccinia striiformis f. sp. hordei, is one of the most important barley (Hordeum vulgare) diseases in the United States. The disease is best controlled using resistant cultivars. Barley genotype Grannenlose Zweizeilige (GZ) has a recessive gene (rpsGZ) that is effective against all races of P. striiformis f. sp. hordei identified so far in the USA. To develop a molecular map for mapping the gene, F(8 )recombinant inbred lines (RILs) were developed from the Steptoe X GZ cross through single-seed descent. Seedlings of the parents and RILs were evaluated for resistance to races PSH-14 and PSH-54 of P. striiformis f. sp. hordei under controlled greenhouse conditions. Genomic DNA was extracted from the parents and 182 F(8 )RILs and used for linkage analysis. The resistance gene analog polymorphism (RGAP) technique was used to identify molecular markers for rpsGZ. A linkage group for the gene was constructed with 12 RGAP markers, of which two markers co-segregated with the resistance locus, and two markers were closely linked to the locus with a genetic distance of 0.9 and 2.0 cM, respectively. These four markers were present only in the susceptible parent. The closest marker to the resistance allele was 11.7 cM away. Analyses of two sets of barley chromosome addition lines of wheat with the two RGAP markers that were cosegregating with the susceptibility allele showed that rpsGZ and the markers were located on the long arm of barley chromosome 4H. Further, tests with four simple sequence repeat (SSR) markers confirmed the chromosomal location of the rpsGZ gene and also integrated the RGAP markers into the known SSR-based linkage map of barley. The closest SSR marker EBmac0679 had a genetic distance of 7.5 cM with the gene in the integrated linkage map constructed with the 12 RGAP markers and 4 SSR markers. The information on chromosomal location and molecular markers for rpsGZ should be useful for incorporating this gene into commercial cultivars and combining it with other resistance genes for durable resistance.

Basidiomycota↗

PubMed2006

Genetic characterization and molecular mapping of Hessian fly resistance genes derived from Aegilops tauschii in synthetic wheat.

Two synthetic hexaploid wheat lines (xAegilotriticum spp., 2n = 6x = 42, genomes AABBDD), SW8 and SW34, developed from the crosses of the durum wheat cultivar Langdon (Triticum turgidum L. var. durum, 2n = 4x = 28, genomes AABB) with two Aegilops tauschii Cosson accessions (2n = 2x = 14, genome DD), were determined to carry Hessian fly [Mayetiola destructor (Say)] resistance genes derived from the Ae. tauschii parents. SW8 was resistant to the Hessian fly biotype Great Plains (GP) and strain vH13 (virulent to H13). SW34 was resistant to biotype GP, but susceptible to strain vH13. Allelism tests indicated that resistance genes in SW8 and SW34 may be allelic to H26 and H13 or correspond to paralogs at both loci, respectively. H26 and H13 were localized to chromosome 4D and 6D, respectively, in previous studies. Molecular mapping in the present study, however, assigned the H26 locus to chromosome 3D rather than 4D. On the other hand, mapping of the resistance gene in SW34 verified the previous assignment of the H13 locus to chromosome 6D. Linkage analysis and physical mapping positioned the H26 locus to the chromosomal deletion bin 3DL3-0.81-1.00. A linkage map for each of these two resistance genes was constructed using simple sequence repeat (SSR) and target region amplification polymorphism (TRAP) markers.

Alleles↗

PubMed2006

Genetic mapping reveals a single major QTL for bacterial wilt resistance in Italian ryegrass (Lolium multiflorum Lam.).

Bacterial wilt caused by Xanthomonas translucens pv. graminis (Xtg) is a major disease of economically important forage crops such as ryegrasses and fescues. Targeted breeding based on seedling inoculation has resulted in cultivars with considerable levels of resistance. However, the mechanisms of inheritance of resistance are poorly understood and further breeding progress is difficult to obtain. This study aimed to assess the relevance of the seedling screening in the glasshouse for adult plant resistance in the field and to investigate genetic control of resistance to bacterial wilt in Italian ryegrass (Lolium multiflorum Lam.). A mapping population consisting of 306 F1 individuals was established and resistance to bacterial wilt was assessed in glasshouse and field experiments. Highly correlated data (r = 0.67-0.77, P < 0.01) between trial locations demonstrated the suitability of glasshouse screens for phenotypic selection. Analysis of quantitative trait loci (QTL) based on a high density genetic linkage map consisting of 368 amplified fragment length polymorphism (AFLP) and simple sequence repeat (SSR) markers revealed a single major QTL on linkage group (LG) 4 explaining 67% of the total phenotypic variance (Vp). In addition, a minor QTL was observed on LG 5. Field experiments confirmed the major QTL on LG 4 to explain 43% (in 2004) to 84% (in 2005) of Vp and also revealed additional minor QTLs on LG 1, LG 4 and LG 6. The identified QTLs and the closely linked markers represent important targets for marker-assisted selection of Italian ryegrass.

Breeding↗

PubMed2006

Genetic relatedness and population differentiation of Himalayan hulless barley (Hordeum vulgare L.) landraces inferred with SSRs.

A set of 107 hulless barley (Hordeum vulgare L. subsp. vulgare) landraces originally collected from the highlands of Nepal along the Annapurna and Manaslu Himalaya range were studied for genetic relatedness and population differentiation using simple sequence repeats (SSRs). The 44 genome covering barley SSRs applied in this study revealed a high level of genetic diversity among the landraces (diversity index, DI = 0.536) tested. The genetic similarity (GS) based UPGMA clustering and Bayesian Model-based (MB) structure analysis revealed a complex genetic structure of the landraces. Eight genetically distinct populations were identified, of which seven were further studied for diversity and differentiation. The genetic diversity estimated for all and each population separately revealed a hot spot of genetic diversity at Pisang (DI = 0.559). The populations are fairly differentiated (theta = 0.433, R(ST) = 0.445) accounting for > 40% of the genetic variation among the populations. The pairwise population differentiation test confirmed that many of the geographic populations significantly differ from each other but that the differentiation is independent of the geographic distance (r = 0.224, P > 0.05). The high level of genetic diversity and complex population structure detected in Himalayan hulless barley landraces and the relevance of the findings are discussed.

Alleles↗

PubMed2006

Genetic mapping of the pear scab resistance gene Vnk of Japanese pear cultivar Kinchaku.

Pear scab (caused by Venturia nashicola) is one of the most harmful diseases of pears, especially Japanese and Chinese pear species. The molecular identification and early selection of resistant plants could greatly improve pear breeding. We have identified the position of the scab resistance gene, designated Vnk in an indigenous Japanese pear cultivar Kinchaku, within the pear genome by using simple sequence repeat (SSR) markers derived from pear and apple. The position of Vnk was identified in the central region of linkage group 1 of Kinchaku. Several amplified fragment length polymorphism (AFLP) markers linked to Vnk were obtained by bulked segregant analysis. Among them, the AFLP marker closest to Vnk was converted into a sequence tagged site (STS) marker. Four random amplified polymorphic DNA (RAPD) markers previously found to be loosely associated with Vnk (Iketani et al. 2001) were successfully converted into STS markers. Six markers (one SSR Hi02c07 and five STSs converted from AFLP and RAPD) showed tight linkages to Vnk, being mapped with distances ranging from 2.4 to 12.4 cM. The SSR CH-Vf2, which was isolated from a BAC clone of the contig containing the apple scab gene Vf, was mapped at the bottom of linkage group 1 in Kinchaku, suggesting that the Vnk and Vf loci are located in different genomic regions of the same homologous linkage group.

Ascomycota↗

PubMed2006

Identification and fine mapping of AvrPi15, a novel avirulence gene of Magnaporthe grisea.

Avirulence of Magnaporthe grisea isolate CHL346 on rice cultivar GA25 was studied with 242 ascospore progenies derived from the cross CHL346 x CHL42. Segregation analysis of the avirulence in the progeny population was in agreement with the existence of a single avirulence (Avr) gene, designated as AvrPi15. For mapping the Avr gene, we developed a total of 121 microsatellite DNA markers [simple sequence repeat (SSR)], which evenly distributed in the whole-genome of M. grisea through bioinformatics analysis (BIA) using the publicly available sequence. Linkage analysis of the AvrPi15 gene with these SSR markers showed that six markers on chromosome 6, MS6-1, MS6-2, MS6-3, MS6-7, MS6-8 and MS6-10, were linked to the AvrPi15 locus. To further define the chromosomal location of the AvrPi15 locus, two additional markers, MS6-17 and STS6-6, which were developed based on the sequences of telomeric region 11 (TEL11), were subjected to linkage analysis. The results showed that MS6-17 and STS6-6 were associated with the locus by 3.3 and 0.8 cM, respectively. To finely map the Avr gene, two additional candidate avirulence gene (CAG) markers, CAG6-1 and CAG6-2, were developed based on the gene annotation of the sequence of TEL 11. Linkage analysis of the Avr gene with these two markers revealed that both of them completely cosegregated with the AvrPi15 locus. Finally, this locus was physically mapped into approximately 7.2-kb interval of the TEL11 by BIA using these sequence-ready markers. This is the key step toward positional cloning of the AvrPi15 gene.

Chromosome Segregation↗

PubMed2006

Nucleotide diversity in starch synthase IIa and validation of single nucleotide polymorphisms in relation to starch gelatinization temperature and other physicochemical properties in rice (Oryza sativa L.).

The characteristics of starch, such as gelatinization temperature (GT), apparent amylose content (AAC), pasting temperature (PT) and other physicochemical properties, determine the quality of various products of rice, e.g., eating, cooking and processing qualities. The GT of rice flour is controlled by the alk locus, which has been co-mapped to the starch synthase IIa (SSIIa) locus. In this study, we sequenced a 2,051 bp DNA fragment spanning part of intron 6, exon 7, intron 7, exon 8 and part of 3' untranslated region of SSIIa for 30 rice varieties with diverse geographical distribution and variation in starch physicochemical properties. A total of 24 single nucleotide polymorphisms (SNPs) and one insertion/deletion (InDel) were identified, which could be classified into nine haplotypes. The mean pairwise nucleotide diversity pi was 0.00292, and Watterson's estimator theta was 0.00296 in this collection of rice germplasm. Tajima's D test for selection showed no significant deviation from the neutral expectation (D = - 0.04612, P > 0.10). However, significant associations were found between seven of the SNPs and peak GT (T (p)) at P < 0.05, of which two contiguous SNPs (GC/TT) showed a very strong association with T (p) (P < 0.0001). With some rare exception, this GC/TT polymorphism alone can differentiate rice varieties with high or intermediate GT (possessing the GC allele) from those with low GT (possessing the TT allele). In contrast, none of these SNPs or InDel was significantly associated with amylose content. A further 509 rice varieties with known physicochemical properties (e.g., AAC and PT) and known alleles of other starch synthesizing genes were genotyped for the SSIIa GC/TT alleles. Association analysis indicated that 82% of the total variation of AAC in these samples could be explained by a (CT)n simple sequence repeat (SSR) and a G/T SNP of Waxy gene (Wx), and 62.4% of the total variation of PT could be explained by the GC/TT polymorphism. An additional association analysis was performed between these molecular markers and the thermal and retrogradation properties for a subset of 245 samples from the 509 rice varieties. The SSIIa GC/TT polymorphism explained more than 60% of the total variation in thermal properties, whereas the SSR and SNP of Wx gene explained as much as the SSIIa GC/TT of the total variation in retrogradation properties. Our study provides further support for the utilization of the GC/TT polymorphism in SSIIa. As shown in our study of 509 rice varieties, the GC/TT SNP could differentiate rice with high or intermediate GT from those with low GT in about 90% of cases. Using four primers in a single PCR reaction, the GC/TT polymorphism can be surveyed on a large scale. Thus, this SNP polymorphism can be very useful in marker-assisted selection for the improvement of GT and other physicochemical properties of rice.

Agriculture↗

PubMed2006

Diversity arrays technology (DArT) for high-throughput profiling of the hexaploid wheat genome.

Despite a substantial investment in the development of panels of single nucleotide polymorphism (SNP) markers, the simple sequence repeat (SSR) technology with a limited multiplexing capability remains a standard, even for applications requiring whole-genome information. Diversity arrays technology (DArT) types hundreds to thousands of genomic loci in parallel, as previously demonstrated in a number diploid plant species. Here we show that DArT performs similarly well for the hexaploid genome of bread wheat (Triticum aestivum L.). The methodology previously used to generate DArT fingerprints of barley also generated a large number of high-quality markers in wheat (99.8% allele-calling concordance and approximately 95% call rate). The genetic relationships among bread wheat cultivars revealed by DArT coincided with knowledge generated with other methods, and even closely related cultivars could be distinguished. To verify the Mendelian behaviour of DArT markers, we typed a set of 90 Cranbrook x Halberd doubled haploid lines for which a framework (FW) map comprising a total of 339 SSR, restriction fragment length polymorphism (RFLP) and amplified fragment length polymorphism (AFLP) markers was available. We added an equal number of DArT markers to this data set and also incorporated 71 sequence tagged microsatellite (STM) markers. A comparison of logarithm of the odds (LOD) scores, call rates and the degree of genome coverage indicated that the quality and information content of the DArT data set was comparable to that of the combined SSR/RFLP/AFLP data set of the FW map.

Chromosomes, Plant↗

PubMed2006

Tall fescue genomic SSR markers: development and transferability across multiple grass species.

Simple sequence repeat (SSR) markers are highly informative and widely used for genetic and breeding studies. Currently, a very limited number of SSR markers are available for tall fescue (Festuca arundinacea Schreb.) and other forage grass species. A tall fescue genomic library enriched in (GA/CT)( n ) repeats was used to develop primer pairs (PPs) flanking SSRs and assess PP functionality across different forage, cereal, and turf grass species. A total of 511 PPs were developed and assessed for their utility in six different grass species. The parents and a subset of a tall fescue mapping population were used to select PPs for mapping in tall fescue. Survey results revealed that 48% (in rice) to 66% (in tall fescue) of the PPs produced clean SSR-type amplification products in different grass species. Polymorphism rates were higher in tall fescue (68%) compared to other species (46% ryegrass, 39% wheat, and 34% rice). A set of 194 SSR loci (38%) were identified which amplified across all six species. Loci segregating in the tall fescue mapping population were grouped as loci segregating from the female parent (HD28-56, 37%), the male parent (R43-64, 37%), and both parents (26%). Three percent of the loci that were polymorphic between parents were monomorphic in the pseudo F1 mapping population and the remaining loci segregated. Sequencing of amplified products obtained from PP NFFAG428 revealed a very high level of sequence similarity among the grass species under study. Our results are the first report of genomic SSR marker development from tall fescue and they demonstrate the usefulness of these SSRs for genetic linkage mapping in tall fescue and cross-species amplification.

Base Sequence↗

PubMed2006

Microsatellites, single nucleotide polymorphisms and a sequence tagged site in starch-synthesizing genes in relation to starch physicochemical properties in nonwaxy rice (Oryza sativa L.).

Starch characteristics determine the quality of various products of rice, e.g., eating, cooking and processing qualities. Our previous study indicated that molecular markers inside or close to starch synthesizing genes can differentiate the starch properties of 56 waxy rices. Here we report microsatellite (or simple sequence repeat, SSR) polymorphism in the Waxy (Wx) gene, soluble starch synthase I gene (SS1) and starch branching enzyme 1 gene (SBE1), single nucleotide polymorphism (SNP) in Wx and starch branching enzyme 3 gene (SBE3), and a sequence tagged site (STS) in starch branching enzyme 1 gene (SBE1) among 499 nonwaxy rice samples and their relationships with starch physicochemical properties. The nonwaxy rice samples consist of landraces (n = 172) obtained from germplasm centers and cultivars and breeding lines (n = 327) obtained from various breeding programs. Ten (CT)( n ) microsatellite alleles, (CT)(8), (CT)(10), (CT)(11), (CT)(12, )(CT)(17), (CT)(18), (CT)(19), (CT)(20), (CT)(21), and (CT)(22), were found at the Wx locus, of which (CT)(11) was the most frequent, and (CT)(12), (CT)(21) and (CT)(22) were identified for the first time. Four (CT)( n ) microsatellite alleles were found at the SBE1 locus, (CT)(8), (CT)(9), and (CT)(10 )together with an insertion sequence of CTCTCGGGCGA, and (CT)(8) alone without the insertion, of which (CT)(9) and the insertion was a new allele identified in only one rice, IR1552. Multiple microsatellites clustered at the SS1 locus, and in addition to the three alleles previously detected (SSS-A = (AC)(2)...TCC(TC)(11)...(TC)(5)C(ACC)(11), SSS-B = (AC)(3)...TCT(TC)(6)...(TC)(4)C(ACC)(9), and SSS-C = (AC)(3)...TCT(TC)(6)...(TC)(4)C(ACC)(8)), one new allele (SSS-D = (AC)(2)...TCC(TC)(10)...(TC)(4)C(ACC)(9)) was found. Analysis of the starch physicochemical properties of the samples with different microsatellites, SNPs and STS groups indicated that these molecular markers can differentiate almost all the physicochemical properties examined, e.g., apparent amylose content (AAC), pasting viscosity characteristics, and gel textural properties. Wx SSR and Wx SNP alone explained more variations for all physicochemical properties than the other molecular markers. The total six markers could explain 92.2, 81 and 86% of total variation of AAC, gel hardness (HD), and gel cohesiveness (COH), respectively, and they could explain more than 40% of the total variation of hot paste viscosity (HPV), cool paste viscosity (CPV), breakdown viscosity (BD), setback viscosity (SB) and gel adhesiveness (ADH). However, only 29% of the total variation of peak viscosity (PV) and 37% of pasting temperature (PT) could be explained by all the molecular markers. Some of these markers can differentiate the starch physicochemical properties among the rice samples with the same Wx allele, indicating that the variation within Wx allele classes can be explained by other starch synthesizing genes. These SSRs, SNPs and STS are useful in marker-assisted breeding for the improvement of starch quality of rice.

1,4-alpha-Glucan Branching Enzyme↗

PubMed2006

QTL analysis for capsaicinoid content in Capsicum.

Pungency or "heat" found in Capsicum fruit results from the biosynthesis and accumulation of alkaloid compounds known as capsaicinoids in the dissepiment, placental tissue adjacent to the seeds. Pepper cultivars differ with respect to their level of pungency because of quantitative and qualitative variation in capsaicinoid content. We analyzed the segregation of three capsaicinoids: capsaicin, dihydrocapsaicin and nordihydrocapsaicin in an inter-specific cross between a mildly pungent Capsicum annuum 'NuMex RNaky' and the wild, highly pungent C. frutescens accession BG2814-6. F(3) families were analyzed in three trials in California and in Israel and a dense molecular map was constructed comprised mostly of loci defined by simple sequence repeat (SSR) markers. Six QTL controlling capsaicinoid content were detected on three chromosomes. One gene from the capsaicinoid biosynthetic pathway, BCAT, and one random fruit EST, 3A2, co-localized with QTL detected in this study on chromosomes 3 and 4. Because one confounding factor in quantitative determination of capsaicinoid is fruit size, fruit weight measurements were taken in two trials. Two QTL controlling fruit weight were detected, however, they did not co-localize with QTL detected for capsaicinoid content. The major contribution to the phenotypic variation of capsaicinoid content (24-42% of the total variation) was attributed to a digenic interaction between a main-effect QTL, cap7.1, and a marker located on chromosome 2 that did not have a main effect on the trait. A second QTL, cap7.2 is likely to correspond to the QTL, cap, identified in a previous study as having pronounced influence on capsaicinoid content.

Capsaicin↗