Quantitative Trait Loci (QTL) and Candidate Gene Identification for the Non-Darkening Seed Coat Trait in Dry Beans (Phaseolus Vulgaris L.). PDF Download
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Author: Mohammad Erfatpour
Publisher:
ISBN:
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Languages : en
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Seed coat colour is one of the main determinants of seed quality in commercial market classes of dry bean (P. vulgaris L.), including pinto bean. The beige background of the conventional pinto bean seed coat turns brown with age through a process known as postharvest seed coat darkening (PSCD). Beans with darkened seed coat are discounted in the market because they are perceived to be old, hard-to-cook beans. Seed coat darkening (SCD) is attributed to oxidation of proanthocyanidins (PAs) in the seed coat. Breeding for beans with reduced risk of PSCD has been given more attention in recent years because they are appealing to consumers and command higher prices in the market. To achieve this objective, it is important to understand the genetic control of the SCD trait and its relationship with other traits. J is a Mendelian genetic locus known to be responsible for SCD trait in dry beans in which the recessive allele produces a non-darkening (ND) seed coat phenotype. The main objectives of this thesis were to identify quantitative trait loci (QTL) and a gene associated with PSCD in dry beans and understand its function in promoting SCD. A mapping population consisting of 128 F5 recombinant inbred lines (RILs) derived from a cross between a ND cranberry-like bean 'Wit-rood boontje' and a slow-darkening pinto bean '1533-15' was genotyped with an Illumina BARCBEAN6K_3 BeadChip and F5:6 seeds were characterized for seed coat phenotype. A major QTL was identified on chromosome Pv10 which explained 48.1% of the phenotypic variation for seed coat darkening. Amplicon sequencing of 21 candidate genes underlying the QTL revealed a single nucleotide deletion (c.703delG) in the candidate gene Phvul.010G130600 in ND RILs. In silico analysis indicated that Phvul.010G130600 encodes a protein with strong amino acid sequence identity (70%) to a R2R3-MYB-type transcription factor MtPAR, which regulates PA biosynthesis in Medicago truncatula seed coat tissue. The ND trait was correlated with reduced grain yield; however, it is possible to develop high yielding lines. In comparison with the darkening genotypes, the ND genotypes were perceived as sweeter, and had softer and smoother texture and shorter cooking times.
Author: Mohammad Erfatpour
Publisher:
ISBN:
Category :
Languages : en
Pages :
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Book Description
Seed coat colour is one of the main determinants of seed quality in commercial market classes of dry bean (P. vulgaris L.), including pinto bean. The beige background of the conventional pinto bean seed coat turns brown with age through a process known as postharvest seed coat darkening (PSCD). Beans with darkened seed coat are discounted in the market because they are perceived to be old, hard-to-cook beans. Seed coat darkening (SCD) is attributed to oxidation of proanthocyanidins (PAs) in the seed coat. Breeding for beans with reduced risk of PSCD has been given more attention in recent years because they are appealing to consumers and command higher prices in the market. To achieve this objective, it is important to understand the genetic control of the SCD trait and its relationship with other traits. J is a Mendelian genetic locus known to be responsible for SCD trait in dry beans in which the recessive allele produces a non-darkening (ND) seed coat phenotype. The main objectives of this thesis were to identify quantitative trait loci (QTL) and a gene associated with PSCD in dry beans and understand its function in promoting SCD. A mapping population consisting of 128 F5 recombinant inbred lines (RILs) derived from a cross between a ND cranberry-like bean 'Wit-rood boontje' and a slow-darkening pinto bean '1533-15' was genotyped with an Illumina BARCBEAN6K_3 BeadChip and F5:6 seeds were characterized for seed coat phenotype. A major QTL was identified on chromosome Pv10 which explained 48.1% of the phenotypic variation for seed coat darkening. Amplicon sequencing of 21 candidate genes underlying the QTL revealed a single nucleotide deletion (c.703delG) in the candidate gene Phvul.010G130600 in ND RILs. In silico analysis indicated that Phvul.010G130600 encodes a protein with strong amino acid sequence identity (70%) to a R2R3-MYB-type transcription factor MtPAR, which regulates PA biosynthesis in Medicago truncatula seed coat tissue. The ND trait was correlated with reduced grain yield; however, it is possible to develop high yielding lines. In comparison with the darkening genotypes, the ND genotypes were perceived as sweeter, and had softer and smoother texture and shorter cooking times.
Author: Sarita Khanal
Publisher:
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Category :
Languages : en
Pages :
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Author: Dana Robson
Publisher:
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Category :
Languages : en
Pages :
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Several common bean (Phaseolus vulgaris L.) market classes, including cranberry bean, demonstrate seed coat post-harvest darkening (PHD). PHD is associated with poor quality, lowering the overall value of the bean. A candidate MYB was sequenced in darkening (RD) and non-darkening (ND) cranberry bean lines to determine any differences between them. The RD and ND lines were identical for the candidate MYB. An F2 population of a cross between Etna (RD) and Witrood (ND) was created to study the inheritance of the PHD trait and identify its genomic location. The F2 lines were genotyped using Single Nucleotide Polymorphism (SNP) markers and used to develop a linkage map with 11 linkage groups. Multiple QTL Mapping (MQM) identified two QTL associated with colour parameter values on chromosome 10. SNP markers identified with the ND loci may be used in the future for marker assisted selection to develop ND cultivars.
Author: Nicola J. Camp
Publisher: Springer Science & Business Media
ISBN: 1592591760
Category : Medical
Languages : en
Pages : 362
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Book Description
In Quantitative Trait Loci: Methods and Protocols, a panel of highly experienced statistical geneticists demonstrate in a step-by-step fashion how to successfully analyze quantitative trait data using a variety of methods and software for the detection and fine mapping of quantitative trait loci (QTL). Writing for the nonmathematician, these experts guide the investigator from the design stage of a project onwards, providing detailed explanations of how best to proceed with each specific analysis, to find and use appropriate software, and to interpret results. Worked examples, citations to key papers, and variations in method ease the way to understanding and successful studies. Among the cutting-edge techniques presented are QTDT methods, variance components methods, and the Markov Chain Monte Carlo method for joint linkage and segregation analysis.
Author: Joel Ira Weller
Publisher: CABI
ISBN: 1845937341
Category : Technology & Engineering
Languages : en
Pages : 288
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Book Description
Quantitative Trait Loci (QTL) is a topic of major agricultural significance for efficient livestock production. This book covers various statistical methods that have been used or proposed for detection and analysis of QTL and marker-and gene-assisted selection in animal genetics and breeding.
Author: Marcelino Pérez de la Vega
Publisher: Springer
ISBN: 3319635263
Category : Science
Languages : en
Pages : 304
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Book Description
This book provides insights into the genetics and the latest advances in genomics research on the common bean, offering a timely overview of topics that are pertinent for future developments in legume genomics. The common bean (Phaseolus vulgaris L.) is the most important grain legume crop for food consumption worldwide, as well as a model for legume research, and the availability of the genome sequence has completely changed the paradigm of the ongoing research on the species. Key topics covered include the numerous genetic and genomic resources, available tools, the identified genes and quantitative trait locus (QTL) identified, and there is a particular emphasis on domestication. It is a valuable resource for students and researchers interested in the genetics and genomics of the common bean and legumes in general.
Author: Miles Andrew Barrett
Publisher:
ISBN:
Category : Beans
Languages : en
Pages : 270
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Sclerotinia sclerotiorum (Lib.) de Bary is a necrotrophic pathogen capable of causing white mold, a severe disease in common bean. White mold is of particular concern to the Oregon snap bean processing industry, where processors allow less than 3% incidence in harvested shipments. Breeding for white mold resistance in beans has been difficult due to quantitative inheritance and low heritability. We combined two quantitative trait loci (QTL) for physiological resistance to white mold: a QTL located on linkage group 7 from G122 and a B8 QTL from NY6020. The B7 QTL is linked to phaseolin for which a sequence characterized amplified region (SCAR) marker phaseolin has been used successfully to transfer the QTL in dry bean. The transfer in snap bean is more challenging because this QTL is also linked to the p locus which conditions the white-seeded trait. While most snap beans have T phaseolin seed protein, the OSU bush blue lake (BBL) materials have the S form of phaseolin, facilitating the use of T phaseolin as a selectable marker in breeding for white mold resistance. Thus, transfer of this QTL has to be coupled with breaking the linkage between colored seed and the resistance QTL. The B8 QTL is linked to the SS181650 SCAR and AW191200 random amplified polymorphic DNA (RAPD) markers. Oregon State University BBL bean germplasm originally developed with single QTL were crossed to pyramid the two resistance QTL. The assumptions made in combining these two sources of resistance are that the QTL are non-allelic and are additive. OSU 6229, OSU 6230, and OSU 6241 are advanced breeding lines that have the SS181650 allele from NY6020 and show statistically significant higher levels of resistance in the field and greenhouse (straw) test compared to susceptible cultivars. White-seeded, T phaseolin types were selected from a OR 91G x G122 BC2F3 population. The selected lines showed levels of resistance significantly better than the susceptible check cultivars in the straw test. The two sources were crossed and the progeny were subjected to three or more generations of phenotypic selection in the straw test. One hundred and forty eight families were planted in a randomized complete block design (RCBD). All families had been previously genotyped using the PHAS and SS181650 SCAR molecular markers. Plants were inoculated using actively growing mycelium of S. sclerotiorum and scored using a modified straw test to test for genetic additivity among marker classes. None of the lines were statistically more resistant than G122, a QTL donor and standard resistant check. In a separate study, data collected in NY6020-5 x OR 91G and NY6020-5 x OSU 5613 populations suggest that NY6020-5 has a B7 QTL equivalent to G122. Other researchers have presented evidence that G122 has a B8 QTL equivalent to NY6020. Finally in a mixed linear model study we identified two markers, B181500 and C81200, which should prove useful in breeding for white mold resistance. While the material that we developed does not show significantly higher levels of resistance than the resistant parents, we have transferred the resistance QTL into a bush blue lake background, and the lines derived from this work should have significantly higher levels of resistance than existing commercial cultivars. We also present evidence of a QTL not previously identified in NY6020-5.
Author: Esteban Diaz Castro
Publisher:
ISBN:
Category :
Languages : en
Pages :
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Author: Tamara Iva Miller
Publisher:
ISBN: 9781085732857
Category :
Languages : en
Pages :
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The common bean (Phaseolus vulgaris L.) is consumed by millions of people worldwide and is a staple source of protein, starch and micronutrients. Common bean production across the world is affected by abiotic and biotic stresses that limit the growth and yield of this important crop. Efforts to breed improved common bean for dissemination to farmers and consumers in East Africa is underway in several breeding programs worldwide. Improvement on agronomic and consumer traits such as disease resistance can be greatly aided by the application of next generation sequencing technologies. With the decreasing cost of DNA sequencing, genomic re-sequencing of diverse common bean accessions facilitates marker- assisted breeding that can be used to speed the creation of new common bean cultivars. Marker-assisted selection (MAS) is an important aspect of modern bean breeding that seeks to utilize genetic markers to select individuals with improved agronomic and consumer traits. For example, breeders in the African Bean Consortium seek to introgress known genetic loci conferring resistance to multiple diseases into bean genetic backgrounds with preferred seed and agronomic characteristics. However, the usefulness of markers is dependent on whether they are polymorphic in the specific parents of the breeding program. Often genetic markers identified in a specific plant population are not useful for marker assisted selection among a different set of bean parents, which necessitates identification of novel markers linked to the genes of interest that are polymorphic among breeding parents. One disease that greatly affects common bean production in humid tropical and sub-tropical growing regions is Angular Leaf Spot (ALS; caused by the foliar fungus Pseudocercospora griseola Sacc.). Marker assisted breeding is being used in multiple different bean breeding programs to improve the resistance of adapted cultivars to ALS. The ALS resistance locus, Phg-2, is an important resistance locus used to improve plant resistance to Angular Leaf Spot in South America and Pan Africa, however in the case of the African Bean Consortium breeding programs in East Africa, certain bean parents used for breeding were monomorphic for the original marker used to perform marker assisted selection of Phg-2. In order to facilitate marker assisted selection of Phg-2 in specific breeding parents used in the Uganda bean improvement program, an alternative, co-dominant, marker linked to the Phg-2 ALS resistance locus was developed (Chapter 1). A new marker, g796, was identified which is polymorphic among the breeding parents; its co-segregation was confirmed in a segregating F2 population derived from the cross between French bean variety Amy and the ALS resistance donor, Mexico 54. This work was conducted in collaboration with Stephen Kimno and Esther Arunga at Embu University, Kenya, as well as other members of the African Bean Consortium bean breeding programs in Tanzania, Uganda, and Ethiopia. The application of DNA sequencing to marker-assisted breeding and crop improvement is rapidly becoming common in the development of improved bean varieties. A nearly complete reference genome and transcriptome for Phaseolus vulgaris was released in 2014 and newly resequenced genomes of diverse bean accessions are being developed for the purpose of marker assisted breeding. In Chapter 2, whole-genome resequencing of 29 bean accessions, including accessions commonly used as breeding parents, was carried out in collaboration with the Ratz lab at the International Center for Tropical Agriculture (CIAT, Colombia). Genetic diversity analysis was performed in order to access the evolutionary relationships between the sequenced bean genomes. Data generated by this work was made available to the larger bean research community and will be used by breeders and geneticists to perform marker-assisted selection and genetic analysis in the future. Angular leaf spot (ALS) occurs throughout Eastern and Southern Africa (as well as other parts of the world) and can cause yield losses up to 80% in environments that favor the disease. ALS is caused by the fungal pathogen, Pseudocercospora griseola, a highly diverse pathogen with many different races that infect diverse types of bean hosts. Growing crop cultivars with genetic resistance to the disease is one of the most effective measures for farmers to reduce crop losses due to ALS. The landrace Mexico 54 is used as a donor for ALS resistance in East Africa and marker-assisted selection of the Phg-2 ALS resistance locus from Mexico 54 is underway in multiple breeding programs in order to increase the resistance of adapted bean germplasm in East Africa and Brazil. Previous allelism tests between different ALS resistance donors suggested additional resistance loci exist in Mexico 54 besides the Phg-2 locus and were named Phg-5 and Phg-6. The genomic locations of the proposed Phg-5 and Phg-6 resistance genes in Mexico 54 have never been investigated, however, the existence of multiple resistance loci in Mexico 54 is likely the cause of its high level of resistance to ALS on multiple continents. In Chapter 3, a biparental mapping population consisting of 167 F8 recombinant inbred lines (RIL) was derived from a cross between Kablanketi, a preferred bean market type in Tanzania, and Mexico 54 in order to map additional quantitative trait loci that confer resistance to ALS in Mexico 54. The identification of novel ALS resistance loci will aid breeders to develop resistant cultivars as well as provide a greater understanding of the genetic diversity that influences resistance to ALS.
Author: Scott A. Rifkin
Publisher: Humana Press
ISBN: 9781617797866
Category : Medical
Languages : en
Pages : 331
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Book Description
Over the last two decades advances in genotyping technology, and the development of quantitative genetic analytical techniques have made it possible to dissect complex traits and link quantitative variation in traits to allelic variation on chromosomes or quantitative trait loci (QTLs). In Quantitative Trait Loci (QTLs):Methods and Protocols, expert researchers in the field detail methods and techniques that focus on specific components of the entire process of quantitative train loci experiments. These include methods and techniques for the mapping populations, identifying quantitative trait loci, extending the power of quantitative trait locus analysis, and case studies. Written in the highly successful Methods in Molecular BiologyTM series format, the chapters include the kind of detailed description and implementation advice that is crucial for getting optimal results in the laboratory. Thorough and intuitive, Quantitative Trait Loci (QTLs):Methods and Protocols aids scientists in the further study of the links between phenotypic and genotypic variation in fields from medicine to agriculture, from molecular biology to evolution to ecology.
