Alleles In Cultivars Research Articles

Fitness effects and genetic architecture of plant–herbivore interactions in sunflower crop–wild hybrids

*Introgression of cultivar alleles into wild plant populations via crop-wild hybridization is primarily governed by their fitness effects as well as those of linked loci. The fitness of crop-wild hybrids is often dependent on environmental factors, but less is understood about how aspects of the environment affect individual cultivar alleles. *This study investigated the effects of naturally occurring herbivory on patterns of phenotypic selection and the genetic architecture of plant-herbivore interactions in an experimental sunflower crop-wild hybrid population in two locales. *Phenotypic selection analyses suggested that cultivar alleles conferring increased size were generally favored, but at one site cultivar-like flowering time was favored only if three types of herbivory were included in the selection model. Quantitative trait locus (QTL) mapping identified three regions in which the cultivar allele conferred a selective advantage for a number of co-localized traits. Quantitative trait loci for several measures of insect herbivory were detected and, although the cultivar allele increased herbivory damage at the majority of these QTLs, they rarely colocalized with advantageous cultivar alleles for morphological traits. *These results suggest that a subset of cultivar traits/alleles are advantageous in natural environments but that herbivory may mitigate the selective advantage of some cultivar alleles.

Gene-specific markers for the wheat gene Lr34/Yr18/Pm38 which confers resistance to multiple fungal pathogens

The locus Lr34/Yr18/Pm38 confers partial and durable resistance against the devastating fungal pathogens leaf rust, stripe rust, and powdery mildew. In previous studies, this broad-spectrum resistance was shown to be controlled by a single gene which encodes a putative ATP-binding cassette transporter. Alleles of resistant and susceptible cultivars differed by only three sequence polymorphisms and the same resistance haplotype was found in the three independent breeding lineages of Lr34/Yr18/Pm38. Hence, we used these conserved sequence polymorphisms as templates to develop diagnostic molecular markers that will assist selection for durable multi-pathogen resistance in breeding programs. Five allele-specific markers (cssfr1-cssfr5) were developed based on a 3 bp deletion in exon 11 of the Lr34-gene, and one marker (cssfr6) was derived from a single nucleotide polymorphism in exon 12. Validation of reference genotypes, well characterized for the presence or absence of the Lr34/Yr18/Pm38 resistance locus, demonstrated perfect diagnostic values for the newly developed markers. By testing the new markers on a larger set of wheat cultivars, a third Lr34 haplotype, not described so far, was discovered in some European winter wheat and spelt material. Some cultivars with uncertain Lr34 status were re-assessed using the newly derived markers. Unambiguous identification of the Lr34 gene aided by the new markers has revealed that some wheat cultivars incorrectly postulated as having Lr34 may possess as yet uncharacterised loci for adult plant leaf and stripe rust resistance.

Characterization of Oriental Cultivars of Grapevine Using a Reference Allele System of Microsatellite Data and Assignment Test

Six Oriental cultivars of Vitis vinifera, which are native to Japan or China, as well as 2 cultivars of V. labrusca as references, were characterized by 6 microsatellite markers with coded reference alleles. One allele in Oriental cultivars and 3 in V. labrusca have not been reported for Occidental cultivars. Assignment analysis using these data and reported data with grouping of V. labrusca, Oriental cultivars, and vine-growing regions of Occidental cultivars showed that 4 out of 8 Oriental cultivars, but only 3 out of 162 Occidental cultivars, were assigned to Oriental cultivars. These assignments are in accordance with the genetic distances calculated from microsatellite data. These results show that Oriental cultivars have a certain degree of genetic difference from Occidental cultivars within the species V. vinifera.

Identification of cherry incompatibility alleles by microarray

AbstractWe have developed a microarray for identification of sweet cherry incompatibility alleles. Using intron sequence information of the S‐RNase gene, we have created a microarray chip that allows the specific recognition of the incompatibility alleles present in a cultivar. Most of the probes designed showed high specificity towards their alleles. In the original set of probes, cross‐hybridization was observed between a few alleles with high sequence similarity. As our identification system is based on the combined hybridization information from both introns, we were able to identify false positive and unspecific probes which could be eliminated from our microarray. The optimized microarray was tested on cultivars with known alleles. The chip correctly identified all alleles tested. Furthermore, it was also possible to identify alleles in other cultivars where, so far, only one allele has been determined and also to determine in sour cherry the alleles originating from the sweet cherry parent. Our results demonstrate the great promise of microarray technology for this novel application.

Single Nucleotide Polymorphisms and Linkage Disequilibrium in Sunflower

Genetic diversity in modern sunflower (Helianthus annuus L.) cultivars (elite oilseed inbred lines) has been shaped by domestication and breeding bottlenecks and wild and exotic allele introgression(-)the former narrowing and the latter broadening genetic diversity. To assess single nucleotide polymorphism (SNP) frequencies, nucleotide diversity, and linkage disequilibrium (LD) in modern cultivars, alleles were resequenced from 81 genic loci distributed throughout the sunflower genome. DNA polymorphisms were abundant; 1078 SNPs (1/45.7 bp) and 178 insertions-deletions (INDELs) (1/277.0 bp) were identified in 49.4 kbp of DNA/genotype. SNPs were twofold more frequent in noncoding (1/32.1 bp) than coding (1/62.8 bp) sequences. Nucleotide diversity was only slightly lower in inbred lines ( = 0.0094) than wild populations ( = 0.0128). Mean haplotype diversity was 0.74. When extraploted across the genome ( approximately 3500 Mbp), sunflower was predicted to harbor at least 76.4 million common SNPs among modern cultivar alleles. LD decayed more slowly in inbred lines than wild populations (mean LD declined to 0.32 by 5.5 kbp in the former, the maximum physical distance surveyed), a difference attributed to domestication and breeding bottlenecks. SNP frequencies and LD decay are sufficient in modern sunflower cultivars for very high-density genetic mapping and high-resolution association mapping.

Hybrids between cultivated and wild carrots in natural populations in Denmark

Many cultivated plant species are able to hybridize with related wild plants. However, it is not clear whether their hybrids are able to survive and reproduce outside managed fields, and if cultivar genes introgress into wild populations. In areas where wild carrots co-occur with carrot root-crops, pollen and seeds may flow from two different sources in the fields to the surrounding wild populations: from pure cultivar plants that occasionally flower, and from flowering 'bolters' that originate from hybridizations between wild (male) and cultivated carrots (female) in seed production fields in warmer regions of the world. To test whether hybrids are formed and survive in wild Danish populations, and whether prolonged hybridization has led to introgression of cultivar genes, we collected leaf material from adult individuals growing close to carrot fields and analysed their genotypic composition by AFLP. Four hybrids were identified among the 71 plants analysed, and these were most likely F(2) or backcross individuals, sired by pollen from hybrid bolters. Wild populations close to fields were genetically somewhat more similar to cultivars than wild populations far from fields, suggesting that neutral or beneficial cultivar alleles can introgress into the wild gene pool. Despite generations of improvement and adaptation of cultivar carrots to highly managed field conditions, hybrids can thus sometimes survive in wild populations close to carrot fields, and their genes transfer to wild populations by introgression.

Genetic Analysis of Long Chain Synthesis in Rice Amylopectin

The amount of long chains (LC) of amylopectin in high-amylose rice is thought to be one of the important determinants of its quality when cooked. A wide range of differences in LC content have been reported in rice varieties, which can be clearly divided into four classes based on LC and apparent amylose content: namely, amylose and LC-free, low or medium-amylose and low-LC, high-amylose and medium-LC, high-amylose and high-LC. However, genetic factors controlling LC content have not been fully understood. Here, we performed quantitative trait loci (QTL) analysis of LC content using 157 recombinant inbred lines (RILs) derived from a cross of a low-LC cultivar, Hyogokitanishiki, and a high-LC line, Hokuriku 142. By analyzing randomly selected 15 RILs, it was shown that high LC content (≥11%) was associated with high setback viscosity (≥200 RVU), and that low LC (≤ 3%) was associated with low setback viscosity (≤ 130 RVU), as measured by a Rapid Visco Analyzer. With setback viscosity as an indicator for LC content, QTL analysis was conducted using 60 DNA markers including a CAPS marker that distinguished Wx a and Wx b alleles coding for granule-bound starch synthase I (GBSSI or Wx protein), the enzyme working for amylose biosynthesis. Only one QTL with a peak log of likelihood score at the wx locus was detected, and no line showing setback viscosity corresponding to the medium-LC class appeared. The fact that wx mutants of Hokuriku 142 lacked LC in their rice starch supports the view that the functional Wx allele is indispensable for LC synthesis in addition to amylose synthesis in rice endosperm. We suggest three possible reasons why no line with medium-LC content was observed. First, the locus (loci) responsible for generation of medium-LC may be located very close to the wx locus and not able to be dissected by the population and DNA markers we used. Second, there may be special QTLs for medium-LC cultivars that do not exist in low- or high-LC cultivars. Third, medium-LC cultivars may have an as-yet unidentified Wx allele with lower capability in LC synthesis compared to the Wx allele in high-LC cultivars.

PEDIGREE GENOTYPING: A NEW PEDIGREE-BASED APPROACH OF QTL IDENTIFICATION AND ALLELE MINING BY EXPLOITING BREEDING MATERIAL

To date, molecular markers have been made available for many economically important traits. Unfortunately, lack of knowledge of their allelic variation hampers their full exploitation in commercial breeding programs. These markers have usually been identified in one single cross. Consequently, only one or two favourable alleles of the related QTL are identified and may be exploited for marker-assisted breeding (MAB), while a breeding program may include several alleles. Selection for only these alleles means that many favourable genotypes are ignored, which decreases efficiency and leads to genetic erosion. A new approach, called pedigree genotyping, allows the identification and exploitation of the majority of alleles present in an ongoing breeding program. This is achieved by including breeding material itself in QTL detection, so covering multiple generations and linking many crosses through their common ancestors in the pedigree. The principle of Identity by Descent (IBD) is utilised to express the identity of an allele of a modern selection in terms of alleles of founding cultivars. These founder alleles are used as factors in statistical analysis. Co-dominant markers, like SSR (= microsatellite) markers, are essential in this approach since they are able to connect cultivars, breeding selections and progenies at the molecular marker level by monitoring specific chromosomal segments along family trees. Additional advantages of the use of breeding genetic material are (1) a major reduction in experimental costs since plant material is already available and phenotyped by default (2) continuity over generations within breeding programs with regard to marker research (3) the testing of QTL-alleles against a wide range of genetic backgrounds, making results generally applicable (4) possibility to explore intra- as well as inter-QTL interactions. Fruit firmness in apple is used as an example to illustrate the principles of this powerful approach to detect QTLs and estimate their allelic variation. Prospects for strawberry are also indicated

Diversity of evaluated characters and HMW-Glu alleles in landraces and cultivars of emmer, einkorn and spelt wheat

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Molecular and biochemical characterization of puroindoline a and b alleles in Chinese landraces and historical cultivars

Kernel hardness that is conditioned by puroindoline genes has a profound effect on milling, baking and end-use quality of bread wheat. In this study, 219 landraces and 166 historical cultivars from China and 12 introduced wheats were investigated for their kernel hardness and puroindoline alleles, using molecular and biochemical markers. The results indicated that frequencies of soft, mixed and hard genotypes were 42.7, 24.3, and 33.0%, respectively, in Chinese landraces and 45.2, 13.9, and 40.9% in historical cultivars. The frequencies of PINA null, Pinb-D1b and Pinb-D1p genotypes were 43.8, 12.3, and 39.7%, respectively, in hard wheat of landraces, while 48.5, 36.8, and 14.7%, respectively, in historical hard wheats. A new Pinb-D1 allele, designated Pinb-D1t, was identified in two landraces, Guangtouxianmai and Hongmai from the Guizhou province, with the characterization of a glycine to arginine substitution at position 47 in the coding region of Pinb gene. Surprisingly, a new Pina-D1 allele, designated Pina-D1m, was detected in the landrace Hongheshang, from the Jiangsu province, with the characterization of a proline to serine substitution at position 35 in the coding region of Pina gene; it was the first novel mutation found in bread wheat, resulting in a hard endosperm with PINA expression. Among the PINA null genotypes, an allele designed as Pina-D1l, was detected in five landraces with a cytosine deletion at position 265 in Pina locus; while another novel Pina-D1 allele, designed as Pina-D1n, was identified in six landraces, with the characterization of an amino acid change from tryptophan-43 to a 'stop' codon in the coding region of Pina gene. The study of puroindoline polymorphism in Chinese wheat germplasm could provide useful information for the further understanding of the molecular basis of kernel hardness in bread wheat.

Identification, distribution and effects on agronomic traits of the semi-dwarfing Rht alleles in Bulgarian common wheat cultivars

Bulgarian common wheat cultivars released in the period 1925–2003 were studied using the gibberellic acid (GA) test and microsatellite analysis of the Xgwm261 locus on chromosome 2DS to identify the semi-dwarfing (Rht) genes. The old cultivars, isolated through selection from landraces, carried rare alleles (211- and 215-bp) at Xgwm261 locus, and those developed by hybridisation to foreign cultivars, carried the 165- and 174-bp alleles. Forty-two (55.3%) of 76 modern cultivars were GA-responsive. The 192-bp allele, diagnostic for Rht8, was observed in 64 (84.2%) modern cultivars, of which 37 carry Rht8 alone, and 27 possess a combination of Rht8 and a GA-insensitive allele viz. Rht-B1d (17); Rht-D1b (6) and Rht-B1b (4). The 174-bp allele is present in seven cultivars, only one of which is photoperiod-sensitive, and the rest are day-length insensitive. The 203-bp allele was found in six modern cultivars. Cultivars carrying the Rht8 allele are the most widespread and some of them have been cultivated for a long period. Cultivars with the `Saitama 27' allele (Rht-B1d) are the most productive and are second in distribution in the country. The recently observed trend for increasing the proportion of cultivars with GA-insensitive Rht genes is probably due to their combination with the 192-bp allele of Xgwm261 locus tightly linked to the Ppd-D1, to the break of the link between the 174-bp allele and ppd-D1, and to the introduction of other genes influencing flowering time.

PEDIGREE GENOTYPING: A NEW PEDIGREE-BASED APPROACH OF QTL IDENTIFICATION AND ALLELE MINING

To date, molecular markers are available for many economically important traits. Unfortunately, lack of knowledge of the allelic variation of the related genes hampers their full exploitation in commercial breeding programs. These markers have usually been identified in one single cross. Consequently, only one or two favourable alleles of the related QTL are identified and exploitable for marker-assisted breeding (MAB), whereas a breeding program may include several alleles. Selection for just these alleles means that many favourable genotypes are ignored, which decreases efficiency and leads to genetic erosion. A new approach, called Pedigree Genotyping, allows the identification and exploitation of most alleles present in an ongoing breeding program. This is achieved by including breeding material itself in QTL detection, thus covering multiple generations and linking many crosses through their common ancestors in the pedigree. The principle of Identity by Descent (IBD) is utilised to express the identity of an allele of a modern selection in terms of alleles of founding cultivars. These founder alleles are used as factors in statistical analyses. Co-dominant markers like SSR (microsatellite) markers are essential in this approach since they are able to connect cultivars, breeding selections and progenies at the molecular marker level by monitoring specific chromosomal segments along family trees. Additional advantages of the use of breeding genetic material are (1) a major reduction in experimental costs since plant material is already available and phenotyped by default (2) continuity over generations within breeding programs with regard to marker research (3) the testing of QTL-alleles against a wide range of genetic backgrounds, making results generally applicable, (4) intra- as well as inter-QTL interactions can be explored. Fruit firmness in apple will be used as an example to illustrate the principles of this powerful approach to detect QTLs and estimate their allelic variation

Validation of a RAPD marker linked to the anthracnose resistant gene Co-5 in the common bean

Cultivar TU, one of the differential cultivars for anthracnose, carries the resistance gene Co-5 that expresses resistance to a wide range of pathotypes in Brazil. The main goals of this study were to analyze the inheritance of resistance to anthracnose in the cultivar TU in segregating populations derived from crosses with cultivar Ruda, and to validate the random amplified polymorphic DNA (RAPD) marker OPB03 450C , previously identified as being linked to resistance gene Co-5 in cultivar Selection 1360. Results revealed that one single gene present in cultivar TU, Co-5 is responsible for resistance, and that the band of 450 bp of primer OPB03 was linked to it at 15.4 cM. As OPB03 450 is not close enough from the Co-5 gene of TU, it will not be useful during the pyramidation programs. However, this molecular marker can be useful for identification of the Co-5 allele in other cultivars that carry this gene.

Identification of a microsatellite marker associated with Pm3 resistance alleles to powdery mildew in wheat

AbstractThe Pm3 resistance locus, located on chromosome 1A in wheat, confers race‐specific resistance to the obligate biotrophic fungus Blumeria graminis (DC) E.O. Speer f. sp. tritici, the causal agent of powdery mildew. Several Pm3 alleles are still effective in controlling the disease in Europe. A genetic map was constructed to map the Pm3g allele in the recombinant inbred line progeny from the cross ‘RE9001’ (susceptible) בCourtot’ (resistant). Two microsatellite markers were closely mapped to Pm3g. The PSP2999 marker, which cosegregates with this allele, was shown to detect the presence of the Pm3g resistance allele in other cultivars. A collection of 56 wheat cultivars or advanced lines carrying one Pm3 allele was used to assess the allele‐specific amplification of the PSP2999 marker. The same amplification pattern was obtained for lines with Pm3a, Pm3b, Pm3e, Pm3f and Pm3g alleles. Twenty genotypes carrying Pm3d showed a specific amplification pattern. This marker allowed the detection of the Pm3d allele in highly resistant lines whose resistance gene combinations were unknown. It was concluded that PSP2999 is a useful marker to detect Pm3 alleles in parents and to manage them in breeding programmes.

Identification of self-incompatibility alleles in pear cultivars ( Pyrus communis L.)

Self and cross-incompatibility determination by means of fruit and seed set experiments or pollen tube growth observations in the style has been frequently reported to be unclear in pear (Pyrus communis L.). Thus,in order to develop a reliable in vivo method to test pollen-pistil incompatibility in pear, pollen tube performance has been studied along the pistil following self and cross-pollinations. Results show that, while pollen tube growth in the style may be an unclear test, ovule observation at the microscope for the presence of pollen tube in the nucellus is a proper method to test incompatibility in this crop. With this analysis we could identify S-alleles of ‘Williams’ (S1S2) and ‘Coscia’(S3S4), and three of the four possible S-genotypes resulting from the ‘Williams’ × ‘Coscia’ cross, as represented by ‘Butirra Precoz Morettini’ (S1S3), ‘Santa Maria Morettini’ (S2S3)and ‘Tosca’ (S1S4). This result demonstrates that ‘Williams’ and ‘Coscia’ cultivars do not share any allele in common. We also established two new inter-incompatibility groups in pear. Furthermore, the presence of a common allele between ‘Williams’ and ‘Agua de Aranjuez’,and ‘Coscia’ and ‘Agua de Aranjuez’, three apparently unrelated old cultivars, may indicate a narrower genetic base than expected for European pear. This finding together with the fact that 40% of new released cultivars have direct or indirect parental relationship with the cultivars ‘Coscia’ and/or ‘Williams’, anticipates the possibility of new cases of cross-incompatibility for this crop in the future. Both the method described and the determination of the S-genotypes will facilitate the characterisation of self and cross-incompatibility relationships in this species.

Sequence Analysis of the 5′-Terminal Part of GLU-D1 Locus of Landraces and Old Cultivars of Wheat (Triticum aestivum)

We have analyzed 380pb long N-terminal parts of Glu-D1x alleles from several lines of landraces and old cultivars of wheat (Triticum aestivum L.) with the aim to verify, whether alleles characterized as identical according to their mobility in SDS-PAGE are encoded always by the same DNA sequences. European landraces and old cultivars were chosen for the study as a potential source of higher genetic variability as compared with modern wheat cultivars. We have not found any changes in comparison with known data in the sequences of Dx3 and Dx4 alleles, which in fact were rare in the available set of landraces and old cultivars. Three point mutations were found together in Dx2 and Dx5 alleles of landraces and old cultivars, no one in the standard wheat cultivars Chinese Spring and Bezostaya1. Sequencing analysis can be another suitable technique for study of glutenin alleles complementing SDS-PAGE.

The I gene of bean: a dosage-dependent allele conferring extreme resistance, hypersensitive resistance, or spreading vascular necrosis in response to the potyvirus Bean common mosaic virus.

The resistance to the potyvirus Bean common mosaic virus (BCMV) conferred by the I allele in cultivars of Phaseolus vulgaris has been characterized as dominant, and it has been associated with both immunity and a systemic vascular necrosis in infected bean plants under field, as well as controlled, conditions. In our attempts to understand more fully the nature of the interaction between bean with the I resistance allele and the pathogen BCMV, we carefully varied both I allele dosage and temperature and observed the resulting, varying resistance responses. We report here that the I allele in the bean cultivars we studied is not dominant, but rather incompletely dominant, and that the system can be manipulated to show in plants a continuum of response to BCMV that ranges from immunity or extreme resistance, to hypersensitive resistance, to systemic phloem necrosis (and subsequent plant death). We propose that the particular phenotypic outcome in bean results from a quantitative interaction between viral pathogen and plant host that can be altered to favor one or the other by manipulating I allele dosage, temperature, viral pathogen, or plant cultivar.

Abundant Polymorphism in the Flanking Regions of Two Loci for Basic PR-1 Proteins as Markers for indica-aponica Differentiation in Rice (Oryza sativa L.).

In an attempt to use new sources of disease resistance, genomic sequences of two genes Rpr1-1(t) and Rpr1-2(t) of PR-1 proteins, which are one of the major pathogenesis-related (PR) proteins in plants, were obtained by TAIL-PCR on the basis of a registered genomic and from expressed sequence tag (EST) data, respectively. The genetic loci of Rpr1-1(t) and Rpr1-2(t) were identified on chromosome 1 and 5, respectively, using recombinant inbred lines (RILs) from and an indica-japonica cross. Abundant sequence polymorphism between alleles of indica and japonica cultivars were found in the two genes. Polymorphic insertions including the Tnr1 (transposable element in rice #1) sequence in indica cultivars and a minor insertion in japonica cultivars were detected in the ORF flanking regions of Rpr1-1(t). In the ORF flanking regions of Rpr1-2(t), a unique insertion of 827 dp was found in japonica cultivars, while two insertions were found in an indica cultivar, Milyang 23. Despite such diversity in the flanking regions, only a few amino-acid residues were different between the alleles. Based on a test for polymorophism among some cultivars, it was found that variation of inserted/deleted sequences may provide a useful molecular tool for investigating indica-japonica differentiation in rice.

Association Between Dough Quality (W value) and Certain Gliadin Alleles in French Common Wheat Cultivars

No abstract

Automated sizing of fluorescent-labeled simple sequence repeat (SSR) markers to assay genetic variation in soybean

Simple Sequence Repeat (SSR) allele sizing provides a useful tool for genotype identification, pedigree analysis, and for estimating genetic distance between organisms. Soybean [Glycine max (L.) Merr.] cultivars are identified for Plant Variety Protection (PVP) purposes by standard pigmentation and morphological traits. However, many commercial soybeans arise from a limited number of elite lines and are often indistinguishable based on these traits. A system based on SSR markers would provide unique DNA profiles of cultivars. Fluorescent labeling of alleles combined with automated sizing with internal size standards in each gel lane was used as an alternative to standard [32P] labeling to assess genetic variability in soybean. Allelic frequencies at 20 SSR loci were determined in 35 soybean genotypes that account for greater than 95% of the alleles in North American soybean cultivars based upon pedigree analysis. An average of 10.1 alleles per locus (range: 5–17), with a mean gene diversity of 0.80 (range: 0.50 to 0.87) were observed at the 20 SSR loci. The 20 loci successfully distinguished modern soybean cultivars that are identical for morphological and pigmentation traits, as well as 7 soybean genotypes reported to be indistinguishable using 17 RFLP probes. Pedigrees of 7 cultivars were studied to estimate stability of SSRs in soybean across generations. Of the 7 pedigrees 6 had one locus in the progeny with an allele(s) that was not present in either parent. These new alleles are most likely the result of mutation. The mutation rate of SSR alleles in soybean was similar to that reported in humans. To avoid difficulty associated with mutation, DNA fingerprint data should be determined from the bulk of 30-50 plants of a cultivar.