Development of a SCAR Marker Based on SCoT Polymorphisms for Sugarcane Smut Resistance

Sugarcane smut caused by Sporisorium scitanmineumis the most severe sugarcane disease that causes major economic losses in sugarcane production in China, and disease resistance breeding is an important way of preventing and controlling this disease. In this study, BC3F1lines derived from the cross between YC 73-226 and YCE 06-111 were used to generate sugarcane smut-resistant and -susceptible gene pools using bulked segregant analysis (BSA). Eighty-nine random primers of start codon targeted (SCoT) polymorphisms were screened, whereas only primer SCoT44 could stably amplify the specific fragment (HE-Ss44) in the resistant pool. Then, several primer pairs of sequence characterized amplified regions (SCARs) were designed based on the sequence alignment of HE-Ss44 (920 bp), which was recovered after purification, and only one pair of SCAR primers (Ss44-F2/R2, forward: 5'-GGCGGGCACCGTCGAGTCCACAT-3'; reverse: 5'-CCGTCCGTCGG TCTCGTCCTTACG-3') could stably amplify a 400-bp specific band in resistant gene pool and its individuals. A validation test of SCAR marker Ss44-F2/R2 was performed using 34 sugarcane cultivars with known smut resistance, which revealed a selection accuracy of 82.35% between marker detection and known smut resistance. Moreover, Pearson’s correlation analysis also showed that the SCAR marker Ss44-F2/R2 was significantly correlated (r= 0.583, P= 0.0003 < 0.01) with the smut resistance trait in sugarcane. In addition, the nucleotide sequence of HE-Ss44 linked with smut-resistancewas not aligned to the homologous sequence in GenBank (NCBI), and the accession number was MG740763. The SCAR marker Ss44-F2/R2 developed in this study can be used for the rapid detection of smut resistance in sugarcane and may be utilized as reference for the improvement of sugarcane smut resistance based on molecular marker-assisted selection.© 2021 Friends Science Publishers

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Composition of peripheral blood leukocytes and immuno-competent bodies of the cross carp “Petrovsky” in different periods of the fishing season

Rybovodstvo i rybnoe hozjajstvo (Fish Breeding and Fisheries) ◽

10.33920/sel-09-2101-05 ◽

2021 ◽

pp. 58-68

Author(s):

Tatyana Aleksandrovna Suvorova ◽

Galina Iozepovna Pronina ◽

Daniel Veniaminovich Mikrjakov

Keyword(s):

Breeding Season ◽

Peripheral Blood ◽

Visual Fields ◽

Head Kidney ◽

Resistance Breeding ◽

Economic Losses ◽

Blood Leukocytes ◽

Immune Resistance ◽

Fish Breeding ◽

Immunocompetent Organs

Crossing is an effective method of increasing agricultural production. In addition to the productive qualities of the resulting crosses, it is important to maintain and enhance their immune resistance. Breeding for immunity to pathogens of various diseases provides a decrease in economic losses and an increase in breeding efficiency. Cross “Petrovsky” (breeding achievement No. 9153820) is a reciprocal hybrid of Anish Mirror and Chuvash scaled productive carp species. It has been established that this cross is superior to the parental forms in terms of growth intensity and survival of juveniles. The work is devoted to a comparative analysis of the leukocyte composition of peripheral blood and immunocompetent organs of the carp cross “Petrovsky” in different periods of the fish-breeding season. The studies were carried out in late May and early October 2019 in the Kirya breeding farm, Chuvashia (2nd fish breeding zone). In fish, peripheral blood was sampled from the tail vein and tissues of the spleen and head kidney. Blood smears and organ-imprinted smears were taken for the study. The preparations were examined under a light microscope and the leukocyte formula was determined. The study of leukograms of immunocompetent organs and tissues of fish helps to judge the functional state and immune resistance of fish. To determine the index of the abundance of leukocytes in a peripheral blood smear, 100 visual fields were examined in different areas. This indicator allows you to record the intensity of leukopoiesis and indirectly assess the level of leukocytes in a unit of blood volume. Studies have established differences in the proportion of certain types of leukocytes and the intensity of leukopoiesis in different periods of the fish-breeding season. Fish tissues and organs differed in the proportion of lymphocytes, monocytes, and neutrophils. The obtained data can be used in carrying out selection and breeding work aimed at increasing productivity and enhancing the resistance of fish to infectious diseases.

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Molecular marker aided breeding for blast resistant rice in Nepal

Journal of Agriculture and Environment ◽

10.3126/aej.v15i0.19831 ◽

2014 ◽

Vol 15 ◽

pp. 128-138

Author(s):

Bal K Joshi ◽

Hari P Bimb ◽

Gopal Parajuli ◽

Bedanand Chaudhary

Keyword(s):

Resistance Gene ◽

Ssr Markers ◽

Bulked Segregant Analysis ◽

Blast Resistance ◽

Hot Spot ◽

Resistance Breeding ◽

Recurrent Parent ◽

Simple Method ◽

Multiple Alleles ◽

Rice Landraces

Molecular markers tightly linked to target gene have been identified in different chromosomes to impose the genetic selection. This paper summarizes the progress and achievement made in breeding for blast resistance rice based on DNA markers. At least 40 genes conferring resistance to blast isolates with multiple alleles have been described. Both dominant and recessive resistance alleles have been found in many rice landraces. Highly polymorphic and easily detectable SSR markers are being used in breeding for blast resistance. Bulked segregant analysis (BSA) is the simple method for tagging resistance gene by SSR markers. Quantitative trait loci (QTLs) have also been mapped and most of them are linked to qualitative genes. Simple sequence repeat (SSR) markers linked to the gene are being used to select plants possessing the desired trait and markers throughout the genome are being used to select plants that are genetically similar to recurrent parent. Using SSR markers it may be possible to select blast resistance genotypes at any stage of crop development from any small part of crop, to conduct many round of selection, to select without inoculums, without scoring, and without testing in hot spot or artificial inoculation. Molecular based blast resistance breeding work is necessary to initiate in Nepal focusing on resistance gene tagging in Nepalese rice landraces and utilization.

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Developing RAPD Markers for Grape Breeding

HortScience ◽

10.21273/hortsci.31.4.609f ◽

1996 ◽

Vol 31 (4) ◽

pp. 609f-609 ◽

Cited By ~ 1

Author(s):

J. Lu ◽

O. Lamikanra ◽

Y. Wang ◽

Z. Liu ◽

D. Ramming

Keyword(s):

Rapd Markers ◽

Scar Marker ◽

Bulked Segregant Analysis ◽

Rapd Marker ◽

Early Screening ◽

Horticultural Crop ◽

Pooled Dna ◽

Rapd Primer ◽

Breeding Selection ◽

Grape Breeding

The grape is an important horticultural crop that is grown worldwide. Breeding a new grape cultivar by conventional means normally will take several generations of backcross, at least 15 years. The efficiency and speed of selection can be accelerated if genetic markers are available for early screening. This project is designed to generate RAPD markers linked to viticulturally important traits, including seedlessness and pistillate genes. A F1 population with 64 progenies of V. vinifera was used for the RAPD analysis. Bulked Segregant Analysis (BSA) method was used for RAPD primer screening. Three-hundred primers were screened between the two pairs of pooled DNA samples, seeded and seedlessness, pistillate and perfect flowers. At least 10 primers produced one polymorphism each between the pools. Further analysis revealed that one of these RAPDs cosegregated tightly with the seedlessness trait, while the others either had loose linkage or no linkage to the traits. To make the RAPD marker useful for breeding selection, an attempt was made to convert it into SCAR marker. The results demonstrated that the RAPD marker may be useful for grape breeding and interpreting inheritance of a particular trait in grapes.

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Linkage Mapping in a Watermelon Population Segregating for Fusarium Wilt Resistance

Journal of the American Society for Horticultural Science ◽

10.21273/jashs.126.3.344 ◽

2001 ◽

Vol 126 (3) ◽

pp. 344-350 ◽

Cited By ~ 24

Author(s):

Leigh K. Hawkins ◽

Fenny Dane ◽

Thomas L. Kubisiak ◽

Billy B. Rhodes ◽

Robert L. Jarret

Keyword(s):

Ssr Markers ◽

Fusarium Wilt ◽

Rapd Markers ◽

Bulked Segregant Analysis ◽

Citrullus Lanatus ◽

Linkage Groups ◽

Mendelian Segregation ◽

Marker Loci ◽

Resistance Trait ◽

Effective Use

Isozyme, randomly amplified polymorphic DNA (RAPD), and simple sequence repeats (SSR) markers were used to generate a linkage map in an F2 and F3 watermelon [Citrullus lanatus (Thumb.) Matsum. & Nakai] population derived from a cross between the fusarium wilt (Fusarium oxysporum f. sp. niveum) susceptible `New Hampshire Midget' and resistant PI 296341-FR. A 112.9 cM RAPD-based map consisting of 26 markers spanning two linkage groups was generated with F2 data. With F3 data, a 139 cM RAPD-based map consisting of 13 markers covering five linkage groups was constructed. Isozyme and SSR markers were unlinked. About 40% to 48% of the RAPD markers were significantly skewed from expected Mendelian segregation ratios in both generations. Bulked segregant analysis and single-factor analysis of variance were employed to identify RAPD markers linked to fusarium wilt caused by races 1 and 2 of F. oxysporum f. sp. niveum. Current linkage estimates between the resistance trait and the marker loci were too large for effective use in a marker-assisted selection program.

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Identification of novel rice blast resistance alleles through sequence-based allele mining

10.21203/rs.2.18859/v1 ◽

2019 ◽

Author(s):

Ying Zhou ◽

Fang Lei ◽

Qiong Wang ◽

Weicong He ◽

Yuan Bin ◽

...

Keyword(s):

Resistance Genes ◽

Rice Blast ◽

Blast Resistance ◽

Resistance Breeding ◽

Economic Losses ◽

The Novel ◽

Allele Mining ◽

Rice Varieties ◽

Rice Blast Resistance ◽

Blast Resistance Genes

Abstract Background: As rice ( Oryza sativa ) is the staple food of more than half the world’s population, rice production contributes greatly to global food security. Rice blast caused by the fungus M agnaporthe oryzae is a devastating fungal disease of rice, affecting yield and grain quality and resulting in substantial annual economic losses. Because the fungus evolves rapidly,, resistance conferred by most of the single blast race resistance genes is often broken after a few years of intensive agricultural use. Effective resistance breeding in rice therefore requires continual enrichment of the reservoir of resistance genes and alleles. Seed banks represent a rich source of genetic diversity; however, they have not been extensively used to identify novel genes and alleles. Results: We carried out a large-scale screen for novel blast resistance alleles in 1883 rice varieties from major rice producing areas across China. Of these, 107 varieties showed at least moderate resistance to natural infection by rice blast at rice blast nurseries in Enshi and Yichang, Hubei Province. Using sequence-based allele mining to amplify and clone the allelic variants of major rice blast resistance genes at the Pi2/9/gm/zt locus of chromosome 6 from the 107 blast-resistant varieties, we identified 13 novel blast resistance alleles. We then used controlled infections to assess the resistance of rice varieties carrying the novel alleles to 34 single rice blast isolates from Hubei, Guangdong, Jiangsu, Hunan, Jangxi, Sichuan, Heilongjiang, and Fujin Provinces. The varieties identified as being resistant in the nursery trials showed varied disease responses when infected with the single blast isolates, suggesting that the novel Pi2/9/gm/zt alleles vary in their blast resistance spectra. Some of the newly identified alleles have unique single nucleotide polymorphisms (SNPs), insertions, or deletions, in addition to polymorphic residues that are shared between the different alleles. Conclusions: These alleles expand the allelic series of blast resistance genes, enriching the genetic resource for rice blast resistance breeding programs and for studies aimed at deciphering rice–rice blast molecular interactions. Key words : Pi9 , R-genes, Nucleotide diversity, Gene conversion, Resistance gene alleles, Rice blast

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IDENTIFICATION OF A SCAR MARKER LINKED TO A SHATTERING RESISTANCE TRAIT IN SESAME

Turkish Journal Of Field Crops ◽

10.17557/tjfc.359707 ◽

2017 ◽

Author(s):

Chalermpol PHUMICHAI ◽

Weerachai MATTHAYATTHAWORN ◽

Nipha CHUENPOM ◽

Arunee WONGKAEW ◽

Phakaked SOMSAENG ◽

...

Keyword(s):

Scar Marker ◽

Resistance Trait

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Population genetic analyses of Phytophthora cinnamomi reveals three lineages and movement between natural vegetation and avocado orchards in South Africa

Phytopathology ◽

10.1094/phyto-10-21-0414-r ◽

2022 ◽

Author(s):

Juanita Engelbrecht ◽

Tuan A. Duong ◽

Trudy Paap ◽

Joseph Michael Hulbert ◽

Juanita Joyce Hanneman ◽

...

Keyword(s):

South Africa ◽

Genetic Diversity ◽

Phytophthora Cinnamomi ◽

Resistance Breeding ◽

Natural Vegetation ◽

Economic Losses ◽

Western Cape ◽

Natural Ecosystems ◽

Agricultural Industries ◽

Production Areas

Phytophthora cinnamomi is the causal agent of root rot, canker and dieback of thousands of plant species around the globe. This oomycete not only causes severe economic losses to forestry and agricultural industries, but also threatens the health of various plants in natural ecosystems. In this study, 380 isolates of P. cinnamomi from four avocado production areas and two regions of natural vegetation in South Africa were investigated using 15 microsatellite markers. These populations were found to have a low level of genetic diversity and consisted of isolates from three lineages. Shared genotypes were detected between isolates from avocado orchards and natural vegetation, indicating the movement of isolates between these areas. The population from the Western Cape natural vegetation had the highest genotypic diversity and unique alleles, indicating this could be the point of introduction of P. cinnamomi to South Africa. Index of association analysis suggested that five out of six populations were under linkage disequilibrium suggesting a clonal mode of reproduction whereas genotypes sampled from a recently established avocado orchard in the Western Cape were derived from a randomly recombined population. This study provided novel insights on the genetic diversity and spread of P. cinnamomi in South Africa. It also reported on the predominance of triploidy in natural occurring populations and provided evidence for recombination of P. cinnamomi for the first time. The presence of two dominant genotypes in all avocado production areas in South Africa highlight the importance of considering them in disease management and resistance breeding programmes.

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Characterization of a type IIb sodium-phosphate cotransporter from zebrafish (Danio rerio) kidney

AJP Renal Physiology ◽

10.1152/ajprenal.00356.2002 ◽

2003 ◽

Vol 284 (4) ◽

pp. F727-F736 ◽

Cited By ~ 27

Author(s):

C. Graham ◽

P. Nalbant ◽

B. Schölermann ◽

H. Hentschel ◽

R. K. H. Kinne ◽

...

Keyword(s):

Danio Rerio ◽

Molecular Mapping ◽

Functional Characterization ◽

Structural Similarity ◽

Start Codon ◽

Binding Motif ◽

Intestinal Epithelia ◽

Rapid Amplification ◽

Specific Fragment ◽

And Function

Zebrafish (Danio rerio) express two isoforms of the type IIb Na-dependent Pi cotransporter (NaPi). Type NaPi-IIb1 has previously been cloned and characterized. Here, we report the cloning of the NaPi-IIb2 transcript from zebrafish kidney, its localization, and its functional characterization. RT-PCR with renal RNA and degenerate NaPi-IIb-specific primers resulted in a specific fragment. 3′-Rapid amplification of cDNA ends yielded a product that contained typical NaPi-IIb characteristics such as a cysteine-rich COOH terminus and a PDZ (PSD95- Dlg-zona occludens-1) binding motif. Several approaches were unsuccessful at cloning the 5′ end of the transcript; products lacked an in-frame start codon. The missing information was obtained from an EST (GenBank accession number AW423104 ). The combined clone displayed a high degree of homology with published type IIb cotransporter sequences. Specific antibodies were raised against a COOH-terminal epitope of both NaPi-IIb1 and NaPi-IIb2 isoforms. Immunohistochemical mapping revealed apical expression of both isoforms in zebrafish renal and intestinal epithelia, as well as in bile ducts. The novel clone was expressed in oocytes, and function was assayed by the two-electrode voltage-clamp technique. The function of the new NaPi-IIb2 clone was found to be significantly different from NaPi-IIb1 despite strong structural similarities. NaPi-IIb2 was found to be strongly voltage sensitive, with higher affinities for both sodium and phosphate than NaPi-IIb1. Also, NaPi-IIb2 was significantly less sensitive to external pH than NaPi-IIb1. The strong structural similarity but divergent function makes these zebrafish transporters ideal models for the molecular mapping of functionally important regions in the type II NaPi-cotransporter family.

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Characterization of Geminivirus Resistance in an Accession of Capsicum chinense Jacq.

Molecular Plant-Microbe Interactions ◽

10.1094/mpmi-06-10-0126 ◽

2011 ◽

Vol 24 (2) ◽

pp. 172-182 ◽

Cited By ~ 23

Author(s):

Marco A. García-Neria ◽

Rafael F. Rivera-Bustamante

Keyword(s):

Systemic Acquired Resistance ◽

Acquired Resistance ◽

Resistance Breeding ◽

Marker Genes ◽

Oxygen Species ◽

Breeding Programs ◽

Viral Movement ◽

Resistance Trait ◽

Defensive Mechanism

Pepper golden mosaic virus (PepGMV) and Pepper huasteco yellow vein virus (PHYVV), members of the Geminiviridae family, are important pathogens of pepper (Capsicum annuum L.) and other solanaceous crops. Accession BG-3821 of C. chinense Jacq. was reported earlier as resistant to mixed infection with PepGMV and PHYVV. In this work, we characterized the Geminivirus resistance trait present in BG-3821. Segregation analysis suggested that resistance depends on two genes. Our data showed that PepGMV replication in protoplast of resistant plants is approximately 70% lower when compared with the levels observed in protoplasts from susceptible plants. Additionally, viral movement is less efficient in resistant plants. We also evaluated several characteristics commonly associated with systemic acquired resistance (SAR), which is a conserved defensive mechanism. The concentration of salicylic acid was higher in resistant plants inoculated with PepGMV than in susceptible plants. Marker genes for SAR were induced after inoculation with PepGMV in resistant leaves. Similarly, we found a higher accumulation of reactive oxygen species on resistant leaves compared with susceptible ones. A model for the mechanism acting in the Geminivirus resistance detected in BG-3821 is proposed. Finally, the importance of BG-3821 in Geminivirus resistance breeding programs is discussed.

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