Comparison of Anthracnose Resistance with the Presence of Two SCAR Markers Associated with the Rca2 Gene in Strawberry

Strawberry anthracnose diseases are caused primarily by three Colletotrichum species: C. acutatum J.H. Simmonds, C. fragariae A.N. Brooks, and C. gloeosporioides (Penz.) Penz. & Sacc. Molecular markers are being used in breeding programs to identify alleles linked to disease resistance and other positive agronomic traits. In our study, strawberry cultivars and breeding germplasm with known anthracnose susceptibility or resistance to the three anthracnose-causing Colletotrichum species were screened for two sequence characterized amplified region (SCAR) markers linked to the Rca2 gene. The Rca2 resistant allele SCAR markers were associated with varying degrees of significance for a strawberry plant’s anthracnose resistance to C. fragariae but not to C. acutatum or C. gloeosporioides. Although the presence or absence of the markers associated with the Rca2 resistance gene is an imperfect indicator of anthracnose resistance, it may serve as a useful starting point in selecting germplasm for breeding programs.

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PCR-based molecular markers for identification of taxa from the Calypogeia fissa complex (Jungermanniopsida, Calypogeiaceae)

Biodiversity Research and Conservation ◽

10.2478/v10119-012-0024-3 ◽

2012 ◽

Vol 28 (1) ◽

pp. 9-18 ◽

Cited By ~ 1

Author(s):

Katarzyna Buczkowska ◽

Patrycja Gonera ◽

Bartosz Hornik

Keyword(s):

Molecular Markers ◽

Dna Sequences ◽

Scar Marker ◽

Issr Markers ◽

Genetic Differences ◽

Scar Markers ◽

Sequence Characterized Amplified Region ◽

Pcr Product ◽

Isozyme Loci ◽

Diagnostic Traits

Abstract Within Calypogeia fissa, two subspecies connected with geographic distribution are formally recognized: C. fissa subsp.fissa in Europe and C. fissa subsp.neogea in North America. Isoenzyme studies have shown that the European subspecies is genetically differentiated and composed of three genetically distinct groups PS, PB and G. The PS group has the most distinctive morphological features, but no morphological diagnostic traits have been found for groups PB and G. The sequence characterized amplified region (SCAR) markers developed on the basis of ISSR markers, applied in the study, allowed the delimitation of all groups distinguished in Europe within the C. fissa complex (PS, PB and G). The markers also revealed genetic differences between the European and American subspecies. Five primer pairs (Cal01, Cal03-Cal06) of the six pairs studied are useful as the diagnostic tool for the identification of particular groups from the C.fissa complex. The examined SCAR markers showed that the PS group of C.fissa subsp.fissa was the most distinct; it differed from both groups PB and G as well as from C.fissa subsp.neogea. All plants determined on the basis of diagnostic isozyme loci as the PS group amplified a longer product (380 bp) of the Cal04 primer pair than the rest of studied groups and yielded no amplification products in Cal03, Cal05 and Cal06 primers. The primer pair Cal03 distinguished the plants of the PB group from the remaining groups, since only the PB group generated a PCR product of about 290 bp. The genetic differences between all four studied groups of the C.fissa complex were supported by DNA sequences of the SCAR marker Cal04.

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Development of Race-Specific SCAR Markers for Detection of Chinese Races CYR32 and CYR33 of Puccinia striiformis f. sp. tritici

Plant Disease ◽

10.1094/pdis-94-2-0221 ◽

2010 ◽

Vol 94 (2) ◽

pp. 221-228 ◽

Cited By ~ 7

Author(s):

Baotong Wang ◽

Xiaoping Hu ◽

Qiang Li ◽

Baojun Hao ◽

Bo Zhang ◽

...

Keyword(s):

Molecular Markers ◽

Stripe Rust ◽

Genomic Dna ◽

Puccinia Striiformis ◽

Random Amplified Polymorphic Dna ◽

Scar Markers ◽

Wheat Stripe Rust ◽

Wheat Genotypes ◽

Sequence Characterized Amplified Region ◽

Wheat Leaves

Wheat stripe rust, caused by Puccinia striiformis f. sp. tritici, is a devastating disease in China. Races CYR32 and CYR33 have been predominant in the recent P. striiformis f. sp. tritici population. To develop molecular markers for these races, initially 86 isolates, most of which were collected in 2007 throughout China, were tested on the set of wheat genotypes for differentiating Chinese P. striiformis f. sp. tritici races, and their genomic DNA were amplified with 94 random amplified polymorphic DNA (RAPD) primers. Twelve isolates were identified as CYR33, 14 as CYR32, and 60 as 13 other races. A 320-bp band was identified to be associated with CYR32 with primer S1271 (5′-CTTCTCGGTC-3′), and a 550-bp band was identified to be specific to CYR33 with primer S1304 (5′-AGGAGCGACA-3′). The two bands were cloned and sequenced. Based on the sequences, sequence characterized amplified region (SCAR) markers CYR32sp1/sp2 and CYR33sp1/sp2 were developed to differentiate CYR32 and CYR33, respectively, from other races. The SCAR markers were validated with DNA samples from wheat leaves inoculated with selected isolates from the 86 isolates and urediniospore DNA samples from an additional 63 isolates collected from 2006 to 2009. The detection of CYR32 and CYR33 with the SCAR markers was completely consistent with the results of the race identification with the set of differential wheat genotypes. Thus, the markers are highly reliable for identification of the two races.

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Genetic variability of hull-less barley accessions based on molecular and quantitative data

Pesquisa Agropecuária Brasileira ◽

10.1590/s0100-204x2015000200008 ◽

2015 ◽

Vol 50 (2) ◽

pp. 160-167 ◽

Cited By ~ 2

Author(s):

Ricardo Meneses Sayd ◽

Renato Fernando Amabile ◽

Fabio Gelape Faleiro ◽

Graciele Bellon

Keyword(s):

Molecular Markers ◽

Genetic Variability ◽

Quantitative Data ◽

Quantitative Traits ◽

Agronomic Traits ◽

The Other ◽

Brazilian Cerrado ◽

Breeding Programs ◽

Barley Genotypes ◽

Selection Of

The objective of this work was to characterize and quantify the genetic, molecular, and agronomic variability of hull-less barley genotypes, for the selection of parents and identification of genotypes adapted to the irrigated production system in the Brazilian Cerrado. Eighteen hull-less barley accessions were evaluated, and three covered barley accessions served as reference. The characterization was based on 157 RAPD molecular markers and ten agronomic traits. Genetic distance matrices were obtained based on molecular markers and quantitative traits. Graphic grouping and dispersion analyses were performed. Genetic, molecular, and agronomic variability was high among genotypes. Ethiopian accessions were genetically more similar, and the Brazilian ones were genetically more distant. For agronomic traits, two more consistent groupings were obtained, one with the most two-rowed materials, and the other with six-rowed materials. The more diverging materials were the two-rowed CI 13453, CN Cerrado 5, CN Cerrado 1, and CN Cerrado 2. The PI 356466, CN Cerrado 1, PI 370799, and CI 13453 genotypes show agronomic traits of interest and, as genetically different genotypes, they are indicated for crossing, in breeding programs.

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From Genetic Maps to QTL Cloning: An Overview for Durum Wheat

Plants ◽

10.3390/plants10020315 ◽

2021 ◽

Vol 10 (2) ◽

pp. 315

Author(s):

Pasqualina Colasuonno ◽

Ilaria Marcotuli ◽

Agata Gadaleta ◽

Jose Miguel Soriano

Keyword(s):

Molecular Markers ◽

Durum Wheat ◽

Agronomic Traits ◽

Sequence Data ◽

Current Knowledge ◽

Wheat Breeding ◽

Genetic Maps ◽

Breeding Programs ◽

Qtl Fine Mapping ◽

Candidate Loci

Durum wheat is one of the most important cultivated cereal crops, providing nutrients to humans and domestic animals. Durum breeding programs prioritize the improvement of its main agronomic traits; however, the majority of these traits involve complex characteristics with a quantitative inheritance (quantitative trait loci, QTL). This can be solved with the use of genetic maps, new molecular markers, phenotyping data of segregating populations, and increased accessibility to sequences from next-generation sequencing (NGS) technologies. This allows for high-density genetic maps to be developed for localizing candidate loci within a few Kb in a complex genome, such as durum wheat. Here, we review the identified QTL, fine mapping, and cloning of QTL or candidate genes involved in the main traits regarding the quality and biotic and abiotic stresses of durum wheat. The current knowledge on the used molecular markers, sequence data, and how they changed the development of genetic maps and the characterization of QTL is summarized. A deeper understanding of the trait architecture useful in accelerating durum wheat breeding programs is envisioned.

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Development of SCAR Markers Linked to a Phytophthora fragariae Resistance Gene and Their Assessment in European and North American Strawberry Genotypes

Journal of the American Society for Horticultural Science ◽

10.21273/jashs.125.3.330 ◽

2000 ◽

Vol 125 (3) ◽

pp. 330-339 ◽

Cited By ~ 31

Author(s):

K.M. Haymes ◽

W.E. Van de Weg ◽

P. Arens ◽

J.L. Maas ◽

B. Vosman ◽

...

Keyword(s):

North American ◽

Scar Markers ◽

Breeding Programs ◽

Coupling Phase ◽

Repulsion Phase ◽

Sequence Characterized Amplified Region ◽

Scar Primer ◽

Phytophthora Fragariae ◽

Red Stele ◽

Selection Of

Two dominant sequence characterized amplified region (SCAR) markers (linked at 3.0 cM, coupling phase) were constructed for the strawberry (Fragaria ×ananassa Duch.) gene Rpf1. This gene confers resistance to red stele root rot, caused by the soil-born fungus Phytophthora fragariae Hickman var. fragariae. The SCAR markers were developed originally from the sequence of RAPD OPO-16C(438) that is linked in repulsion phase to the Rpf1 allele. This SCAR primer set produced multiple bands in the resistant test progeny and in some of the susceptible progeny; therefore, new SCARs were developed based on the sequence differences among these bands. These new SCARs were linked in coupling phase to the Rpf allele and mapped to the same location as the original RAPD OPO-16C(438). The SCAR markers, as well as some additional RAPD markers known to be linked to Rpf1, were shown to be highly conserved in linkage to the gene based on examination of 133 European and North American Fragaria L. sp. cultivars and breeding selections. These flanking RAPD and SCAR-PCR markers can be used in breeding programs for the selection of red stele (Rpf1) resistance.

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Development of RAPD-SCAR markers for Lonicera japonica Thunb. (Caprifolicaceae) variety authentication by improved RAPD and DNA cloning

Revista de Biología Tropical ◽

10.15517/rbt.v62i4.13493 ◽

2014 ◽

Vol 62 (4) ◽

pp. 1649 ◽

Cited By ~ 13

Author(s):

Luquan Yang ◽

Md. Asaduzzaman Khan ◽

Zhiqiang Mei ◽

Manman Yang ◽

Tiandan Zhang ◽

...

Keyword(s):

Molecular Markers ◽

Molecular Marker ◽

Scar Marker ◽

Rapd Analysis ◽

Random Amplified Polymorphic Dna ◽

Vital Role ◽

Lonicera Japonica ◽

Scar Markers ◽

Sequence Characterized Amplified Region ◽

Young Leaves

Genetic diversity within a species is a common feature, which plays a vital role in its survival and adaptability, and is important for the identification and authentication of a species. Lonicera japonica is a traditionally used medicinal plant, which have been recently genetically characterized by an improved random ampliﬁed polymorphic DNA (RAPD) analysis. In this study, the molecular markers on the basis of these RAPD fragments have been developed to identify specific L. japonica variety. The DNAs were extracted from fresh young leaves of different samples of L. japonica collected from Shenzhen, Yichang, Leshan, Emei and Loudi, China. The DNA materials were amplified using improved RAPD PCR. Different RAPD bands were excised, cloned and developed for stable sequence-characterized amplified region (SCAR) markers with different species. Two SCAR markers, JYH3-3 and JYH4-3, have been successfully cloned from improved RAPD fragments. The SCAR marker JYH3-3 was found specific for all of the L. japonica samples collected from the different regions, and another marker JYH 4-3 was strictly specific to the Shenzhen sample from Guangdong province, which is geographically distant from Hubei, Sichuan and Hunan Provinces (source of other L. japonica samples). The marker JYH3-3 was found as specific molecular marker for the identification of L. japonica, while JYH4-3 was found as molecular marker strictly specific for the Shenzhen sample. The developed SCAR markers might serve as more specific molecular markers for L. japonica variety authentication. The combination of improved RAPD analysis and SCAR marker development have resulted useful tools to study the genetic variety of any organism, which we have successfully applied here in L. japonica.de cualquier organismo, que hemos aplicado con éxito en L. japonica.

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Identification of PCR-based Molecular Markers Linked to B, A Carotenoid-related Gene in Tomato

HortScience ◽

10.21273/hortsci.33.3.515c ◽

1998 ◽

Vol 33 (3) ◽

pp. 515c-515

Author(s):

Yiping Zhang ◽

John R. Stommel

Keyword(s):

Molecular Markers ◽

Rapd Markers ◽

Significant Contribution ◽

Random Amplified Polymorphic Dna ◽

Isogenic Line ◽

Breeding Programs ◽

Tomato Fruits ◽

Starting Point ◽

Lycopersicon Cheesmanii ◽

Β Carotene

β-carotene is the principal provitamin A caroteniod found in tomato fruits and makes a significant contribution to the fruits nutritional value. The dominant B gene conditions high levels of β-carotene in ripe tomato fruits. PCR-based molecular markers, including random amplified polymorphic DNA (RAPD) and amplified fragment length polymorphism (AFLP), were used to identify marker linkage to the B locus. The study was conducted using a near-isogenic line (NIL) of the cultivar Rutgers isogenic for the B locus and bulk segregant analysis of an interspecific F2 population segregating for the B locus, which was derived from the cross of Lycopersicon cheesmanii accession LA 317 × L. esculentum cv. Floradade. Sixty-four AFLP primer pairs and 1018 arbitrary RAPD primers were screened for polymorphism between the pair of NILs and between the two bulks. A number of amplified RAPD and AFLP products were identified that were present in one line or bulk but not the other. Marker linkage with the B locus was confirmed by checking individual samples from the F2 and BC populations. Two RAPD markers were confirmed tightly linked with the B phenotype using the interspecific F2 population. Similarly, a single AFLP marker was identified with close linkage to the B phenotype using the NIL F2 population. The markers identified in this study can be useful in breeding programs with marker assisted selection and, if very tightly linked, as a starting point to isolate the gene.

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Identification of the Optimum Environments for the High Yield and Quality Traits of Lentil Genotypes Evaluated in Multi-Location Trials

Sustainability ◽

10.3390/su13158247 ◽

2021 ◽

Vol 13 (15) ◽

pp. 8247

Author(s):

Dimitrios N. Vlachostergios ◽

Christos Noulas ◽

Anastasia Kargiotidou ◽

Dimitrios Baxevanos ◽

Evangelia Tigka ◽

...

Keyword(s):

Crude Protein ◽

Agronomic Traits ◽

High Yield ◽

Breeding Programs ◽

Growing Seasons ◽

Yield And Quality ◽

Food And Feed ◽

Superior Genotypes ◽

Selection Of ◽

The Ideal

Lentil is a versatile and profitable pulse crop with high nutritional food and feed values. The objectives of the study were to determine suitable locations for high yield and quality in terms of production and/or breeding, and to identify promising genotypes. For this reason, five lentil genotypes were evaluated in a multi-location network consisting of ten diverse sites for two consecutive growing seasons, for seed yield (SY), other agronomic traits, crude protein (CP), cooking time (CT) and crude protein yield (CPY). A significant diversification and specialization of the locations was identified with regards to SY, CP, CT and CPY. Different locations showed optimal values for each trait. Locations E4 and E3, followed by E10, were “ideal” for SY; locations E1, E3 and E7 were ideal for high CP; and the “ideal” locations for CT were E3 and E5, followed by E2. Therefore, the scope of the cultivation determined the optimum locations for lentil cultivation. The GGE-biplot analysis revealed different discriminating abilities and representativeness among the locations for the identification of the most productive and stable genotypes. Location E3 (Orestiada, Region of Thrace) was recognized as being optimal for lentil breeding, as it was the “ideal” or close to “ideal” for the selection of superior genotypes for SY, CP, CT and CPY. Adaptable genotypes (cv. Dimitra, Samos) showed a high SY along with excellent values for CP, CT and CPY, and are suggested either for cultivation in many regions or to be exploited in breeding programs.

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Meta-QTL analysis and identification of candidate genes for quality, abiotic and biotic stress in durum wheat

Scientific Reports ◽

10.1038/s41598-021-91446-2 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Jose Miguel Soriano ◽

Pasqualina Colasuonno ◽

Ilaria Marcotuli ◽

Agata Gadaleta

Keyword(s):

Molecular Markers ◽

Abiotic Stress ◽

Durum Wheat ◽

Candidate Genes ◽

Biotic Stress ◽

Qtl Analysis ◽

Complex Traits ◽

Genetic Basis ◽

Agronomic Traits ◽

Plant Performance

AbstractThe genetic improvement of durum wheat and enhancement of plant performance often depend on the identification of stable quantitative trait loci (QTL) and closely linked molecular markers. This is essential for better understanding the genetic basis of important agronomic traits and identifying an effective method for improving selection efficiency in breeding programmes. Meta-QTL analysis is a useful approach for dissecting the genetic basis of complex traits, providing broader allelic coverage and higher mapping resolution for the identification of putative molecular markers to be used in marker-assisted selection. In the present study, extensive QTL meta-analysis was conducted on 45 traits of durum wheat, including quality and biotic and abiotic stress-related traits. A total of 368 QTL distributed on all 14 chromosomes of genomes A and B were projected: 171 corresponded to quality-related traits, 127 to abiotic stress and 71 to biotic stress, of which 318 were grouped in 85 meta-QTL (MQTL), 24 remained as single QTL and 26 were not assigned to any MQTL. The number of MQTL per chromosome ranged from 4 in chromosomes 1A and 6A to 9 in chromosome 7B; chromosomes 3A and 7A showed the highest number of individual QTL (4), and chromosome 7B the highest number of undefined QTL (4). The recently published genome sequence of durum wheat was used to search for candidate genes within the MQTL peaks. This work will facilitate cloning and pyramiding of QTL to develop new cultivars with specific quantitative traits and speed up breeding programs.

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Recent advances in CRISPR/Cas9 and applications for wheat functional genomics and breeding

aBIOTECH ◽

10.1007/s42994-021-00042-5 ◽

2021 ◽

Author(s):

Jun Li ◽

Yan Li ◽

Ligeng Ma

Keyword(s):

Functional Genomics ◽

Genome Editing ◽

Functional Annotation ◽

Genome Engineering ◽

Agronomic Traits ◽

Wheat Breeding ◽

Breeding Programs ◽

Base Editing ◽

The World ◽

World Food Security

AbstractCommon wheat (Triticum aestivum L.) is one of the three major food crops in the world; thus, wheat breeding programs are important for world food security. Characterizing the genes that control important agronomic traits and finding new ways to alter them are necessary to improve wheat breeding. Functional genomics and breeding in polyploid wheat has been greatly accelerated by the advent of several powerful tools, especially CRISPR/Cas9 genome editing technology, which allows multiplex genome engineering. Here, we describe the development of CRISPR/Cas9, which has revolutionized the field of genome editing. In addition, we emphasize technological breakthroughs (e.g., base editing and prime editing) based on CRISPR/Cas9. We also summarize recent applications and advances in the functional annotation and breeding of wheat, and we introduce the production of CRISPR-edited DNA-free wheat. Combined with other achievements, CRISPR and CRISPR-based genome editing will speed progress in wheat biology and promote sustainable agriculture.

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