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Author: Felix Eugenio Enciso Rodriguez Publisher: ISBN: 9781392078624 Category : Electronic dissertations Languages : en Pages : 167
Book Description
As a staple food, the potato (Solanum tuberosum L.) plays an important role in human nutrition and it is currently the third most important food crop after rice and wheat. However, the potato crop faces high production losses caused mainly by biotic factors. With the advent of cutting-edge technologies suitable for potatoes, there is an increasing possibility to accelerate genetic progress and variety generation. To contribute to the implementation of genomic strategies to accelerate potato breeding, three different approaches were used. First, whole genome regressions were conducted using additive and dominant allele dosage models for late blight and common scab resistance in tetraploid potatoes. Multiple Single Nucleotide Polymorphisms (SNPs), contribute to late blight resistance, uncovering the introgression history for this trait whereas an unreported locus with a sizable contribution to common scab resistance was detected. Prediction accuracy assessments demonstrated that 90% of the genetic variance could be captured with an additive model, demonstrating the applicability of genomic prediction for tetraploid potato breeding. Second, a genome editing approach was implemented to breakdown the S-RNase -based self incompatibly in diploid potatoes. New S-RNase allelic variants, with flower-restricted expression, were identified in two self-incompatible (SI) diploid potatoes and mapped to chromosome I in a low recombination region. A dual single-guide RNA strategy was used to generate S-RNase knock-out lines producing premature stop codons on each targeted S-RNase allele. Self-compatibility was achieved in T0 knock-outs and stable transmitted to T1 lines. Additionally, Cas-9 free plants were also obtained. Plasticity in the self-compatible response was also observed in wild-type lines, presumably associated with non-stylar and environmental factors. Third, validation of the IPI-O4 -mediated suppression of the RB-based late blight resistance was conducted using in vivo and in vitro approaches. The hypersensitive response (HR) was confirmed when IPI-O1 was co-infiltrated with the RB gene from Solanum bulbocastanum using a heterologous system. However, HR was observed when IPI-O1 and IPI-O4 were infiltrated in transgenic potato lines carrying a synthetic RB gene containing a Coiled-Coil (CC) domain from S. pinnatisectum. Further work should be conducted to confirm this un-reported interaction. Similarly, we could not validate CC-dimerization using yeast-two hybrid assays and therefore more extensive experiments should be conducted to confirm this result. Ultimately, these genomic approaches open a new window to accelerate the generation of new potato varieties. Genomic selection strategies along with targeted mutagenesis will expand the boundaries of both approaches, reducing the potato breeding cycle considerably while maintaining genetic diversity, and providing access to genomic regions with low or null recombination in potatoes.
Author: Felix Eugenio Enciso Rodriguez Publisher: ISBN: 9781392078624 Category : Electronic dissertations Languages : en Pages : 167
Book Description
As a staple food, the potato (Solanum tuberosum L.) plays an important role in human nutrition and it is currently the third most important food crop after rice and wheat. However, the potato crop faces high production losses caused mainly by biotic factors. With the advent of cutting-edge technologies suitable for potatoes, there is an increasing possibility to accelerate genetic progress and variety generation. To contribute to the implementation of genomic strategies to accelerate potato breeding, three different approaches were used. First, whole genome regressions were conducted using additive and dominant allele dosage models for late blight and common scab resistance in tetraploid potatoes. Multiple Single Nucleotide Polymorphisms (SNPs), contribute to late blight resistance, uncovering the introgression history for this trait whereas an unreported locus with a sizable contribution to common scab resistance was detected. Prediction accuracy assessments demonstrated that 90% of the genetic variance could be captured with an additive model, demonstrating the applicability of genomic prediction for tetraploid potato breeding. Second, a genome editing approach was implemented to breakdown the S-RNase -based self incompatibly in diploid potatoes. New S-RNase allelic variants, with flower-restricted expression, were identified in two self-incompatible (SI) diploid potatoes and mapped to chromosome I in a low recombination region. A dual single-guide RNA strategy was used to generate S-RNase knock-out lines producing premature stop codons on each targeted S-RNase allele. Self-compatibility was achieved in T0 knock-outs and stable transmitted to T1 lines. Additionally, Cas-9 free plants were also obtained. Plasticity in the self-compatible response was also observed in wild-type lines, presumably associated with non-stylar and environmental factors. Third, validation of the IPI-O4 -mediated suppression of the RB-based late blight resistance was conducted using in vivo and in vitro approaches. The hypersensitive response (HR) was confirmed when IPI-O1 was co-infiltrated with the RB gene from Solanum bulbocastanum using a heterologous system. However, HR was observed when IPI-O1 and IPI-O4 were infiltrated in transgenic potato lines carrying a synthetic RB gene containing a Coiled-Coil (CC) domain from S. pinnatisectum. Further work should be conducted to confirm this un-reported interaction. Similarly, we could not validate CC-dimerization using yeast-two hybrid assays and therefore more extensive experiments should be conducted to confirm this result. Ultimately, these genomic approaches open a new window to accelerate the generation of new potato varieties. Genomic selection strategies along with targeted mutagenesis will expand the boundaries of both approaches, reducing the potato breeding cycle considerably while maintaining genetic diversity, and providing access to genomic regions with low or null recombination in potatoes.
Author: Jagesh Tiwari Publisher: CRC Press ISBN: 1000823539 Category : Science Languages : en Pages : 463
Book Description
The book delves into post-genomics advances in potato improvement since the potato genome sequencing in 2011. It includes recent developments in the field of potato genetic resources, genes and SNP markers discovery, and the progress in next-generation breeding applying various omics technologies and modern sequencing tools. It covers cutting-edge technologies in potato - a global perspective, genome sequencing and resequencing of various cultivated and wild species, potato germplasm management and characterization, prebreeding genomics, genome mapping and gene cloning, markers discovery, marker-assisted selection, transgenics, microRNAs, transcriptomics, proteomics, metabolomics, phenomics, next-generation potato breeding technologies including genome editing and genomic selection and bioinformatics applications in the post-genomics era in potato. As genome editing and genomic selection have become emerging tools in crop improvement including potato, several research works have been demonstrated and applied world over. This book concentrates on genomics-aided characterization of germplasm and markers discovery to accelerate potato breeding. Further, various omics technologies strengthen our understanding on discovery of new genes/proteins/metabolites and key traits based on high-throughput phenotyping involved in various biotic and abiotic stresses in potato crop. The book is a useful source of information related to genomics-led research and development of this crop. It will serve as a valuable resource for potato researchers working in the area of molecular biology and would be beneficial for college students, PhD scholars, scientists, academicians, farmers and policy makers.
Author: John E. Bradshaw Publisher: Springer Nature ISBN: 3030644146 Category : Science Languages : en Pages : 571
Book Description
The potato (Solanum tuberosum) is the world’s fourth most important food crop after maize, rice and wheat with 377 million tonnes fresh-weight of tubers produced in 2016 from 19.2 million hectares of land, in 163 countries, giving a global average yield of 19.6 t ha-1 (http://faostat.fao.org). About 62% of production (234 million tonnes) was in Asia (191), Africa (25) and Latin America (18) as a result of steady increases in recent years, particularly in China and India. As a major food crop, the potato has an important role to play in the United Nations “2030 Agenda for Sustainable Development” which started on 1 January 2016 (http://faostat.fao.org). By 2030 the aim is to “ensure access by all people, in particular the poor and people in vulnerable situations, including infants, to safe, nutritious and sufficient food all year round”. By then, the world population is expected to reach 8.5 billion and continue to increase to 9.7 billion in 2050. For potatoes, the need is to increase production and improve nutritional value during a period of climate change, a key aspect of which will be the breeding of new cultivars for a wide range of target environments and consumers. The aim of the book is to help this endeavour by providing detailed information in three parts on both the theory and practice of potato breeding. Part I deals with the history of potato improvement and with potato genetics. Part II deals with breeding objectives, divided into improving yield, quality traits and resistance to the most important diseases and pests of potatoes. Part III deals with breeding methods: first, the use of landraces and wild relatives of potato in introgression breeding, base broadening and population improvement; second, breeding clonally propagated cultivars as a way to deliver potato improvement to farmers’ fields; third, as an alternative, breeding potato cultivars for propagation through true potato seed; and fourth, gene editing and genetic transformation as ways of making further improvements to already successful and widely grown cultivars. Included are marker-assisted introgression and selection of specific alleles, genomic selection of many unspecified alleles and diploid F1 hybrid breeding.
Author: Swarup Kumar Chakrabarti Publisher: Springer ISBN: 3319661353 Category : Science Languages : en Pages : 332
Book Description
This book describes the historical importance of potato (Solanum tuberosum L.),potato genetic resources and stocks (including S. tuberosum group Phureja DM1-3 516 R44, a unique doubled monoploid homozygous line) used for potato genome sequencing. It also discusses strategies and tools for high-throughput sequencing, sequence assembly, annotation, analysis, repetitive sequences and genotyping-by-sequencing approaches. Potato (Solanum tuberosum L.; 2n = 4x = 48) is the fourth most important food crop of the world after rice, wheat and maize and holds great potential to ensure both food and nutritional security. It is an autotetraploid crop with complex genetics, acute inbreeding depression and a highly heterozygous nature. Further, the book examines the recent discovery of whole genome sequencing of a few wild potato species genomes, genomics in management and genetic enhancement of Solanum species, new strategies towards durable potato late blight resistance, structural analysis of resistance genes, genomics resources for abiotic stress management, as well as somatic cell genetics and modern approaches in true-potato-seed technology. The complete genome sequence provides a better understanding of potato biology, underpinning evolutionary process, genetics, breeding and molecular efforts to improve various important traits involved in potato growth and development.
Author: Hugo Campos Publisher: Springer Nature ISBN: 3030286835 Category : Science Languages : en Pages : 524
Book Description
This book is open access under a CC BY 4.0 license. This book provides a fresh, updated and science-based perspective on the current status and prospects of the diverse array of topics related to the potato, and was written by distinguished scientists with hands-on global experience in research aspects related to potato. The potato is the third most important global food crop in terms of consumption. Being the only vegetatively propagated species among the world’s main five staple crops creates both issues and opportunities for the potato: on the one hand, this constrains the speed of its geographic expansion and its options for international commercialization and distribution when compared with commodity crops such as maize, wheat or rice. On the other, it provides an effective insulation against speculation and unforeseen spikes in commodity prices, since the potato does not represent a good traded on global markets. These two factors highlight the underappreciated and underrated role of the potato as a dependable nutrition security crop, one that can mitigate turmoil in world food supply and demand and political instability in some developing countries. Increasingly, the global role of the potato has expanded from a profitable crop in developing countries to a crop providing income and nutrition security in developing ones. This book will appeal to academics and students of crop sciences, but also policy makers and other stakeholders involved in the potato and its contribution to humankind’s food security.
Author: Irwin Goldman Publisher: John Wiley & Sons ISBN: 1119828228 Category : Science Languages : en Pages : 477
Book Description
Plant Breeding Reviews presents state-of-the-art reviews on plant genetics and the breeding of all types of crops by both traditional means and molecular methods. Many of the crops widely grown today stem from a very narrow genetic base; understanding and preserving crop genetic resources is vital to the security of food systems worldwide. The emphasis of the series is on methodology, a fundamental understanding of crop genetics, and applications to major crops.
Author: Bidyut Kumar Sarmah Publisher: Springer Nature ISBN: 3030633721 Category : Science Languages : en Pages : 277
Book Description
This book serves the teachers, researchers and the students as a handy and concise reference as well as guidebook while designing and planning for use of the advanced technologies for crop improvement. The content of the book is designed to cover the latest genome engineering techniques for crop improvement. The conventional breeding has got its limitations such as non-availability of desired genes within the genepool. In many cases, breeding has been highly used and it has nearly reached its highest limit so far as the productivity and production of crops are concerned. However, with increasing need of food and decreasing resources, including water, land, labour, etc., to feed the growing population, the alternative available ways of increasing crop productivity need to be explored and exploited. Genome engineering has a wide scope that includes technologies such as genetic engineering and transgenesis, RNA technologies, CRISPR, cisgenics and subgenics for better productivity and more efficient biotic and abiotic stress management. Therefore, the book is planned to enlighten the readers with the advanced technologies with examples and case studies, whenever possible. Efforts will be made to emphasize on general efforts on various major food crops; however, it would also be made clear that such efforts could be taken as proofs of concepts and that this could be extrapolated keeping the demand in mind.
Author: Lin Song (Ph.D.) Publisher: ISBN: Category : Languages : en Pages : 0
Book Description
Breeding gains of commercial autotetraploid potato (Solanum tuberosum L.) have been limited by tetrasomic inheritance for centuries. After mapping a self-compatible gene (Sli) on chromosome 12 at the end of the 20th century, the breeding strategy has shifted towards developing diploid inbred lines that can generate F1 hybrid varieties through sexual hybridization. Overcoming the gametophytic self-incompatibility through Sli is the first step in breeding at the diploid level. Then self-fertilization is performed within each breeding cycle to achieve pure diploid inbred lines. However, reaching full homozygosity is made difficult by severe inbreeding depression in potato. As a result, multiple hybridization events are needed to break linkages with the deleterious alleles. This research aims to create the germplasm and provide the data for future diploid potato breeding. We first focused on genes that were well characterized in potato: Sli and the vine maturity gene StCDF1 (Cycling DOF Factor 1). A modified backcrossing scheme using primary dihaploids of Solanum tuberosum as the recurrent parental background allowed for the selection of self-fertile F2 individuals homozygous for Sli. By integrating haplotype and quantitative trait locus (QTL) analysis, we identified and selected partially inbred lines fixed for the two favorable alleles. They were used to initiate new cycles of selection with the goal of increasing homozygosity while maintaining plant vigor, fertility, and yield. Then we sought to discover new genetic variants by genome-wide association study (GWAS) and joint linkage mapping. Two years of field trials were performed at the Hancock Agricultural Research Station (HARS), WI, using the progeny from Backcross Cycles 1 and 2 (BC1, BC2) in the years 2020 and 2021. The traits evaluated were vine maturity, tuber appearance, tuber yield, tuber size, specific gravity, chip color, and tuber sprouting. 25 significant QTL, including CDF1 and the tuber shape gene StOFP20, were identified in GWAS. Through joint linkage mapping with connected outbred F1 progeny in the 2021 field trial, we determined the three most desirable OFP20 haplotypes for round tuber shape. We further explored the potential of utilizing genomic selection for diploid potato with the two-year field trial data. The narrow-sense heritability estimates ranged from 0.41 to 0.63. Tuber yield showed the highest prediction reliability for marker-assisted genomic selection at 0.78. Both additive and dominance effects were included in the model, and dominance was most important for tuber yield, explaining 12% of the variance through heterosis. We have also discovered that, despite lower prediction accuracy, the historical tetraploid data can be used as a training population to predict traits of diploid potatoes. The prediction ability for diploids with the mixed ploidy training population ranged from 0.1 to 0.3.
Author: Lin Song (Ph.D.) Publisher: ISBN: Category : Languages : en Pages : 0
Book Description
Breeding gains of commercial autotetraploid potato (Solanum tuberosum L.) have been limited by tetrasomic inheritance for centuries. After mapping a self-compatible gene (Sli) on chromosome 12 at the end of the 20th century, the breeding strategy has shifted towards developing diploid inbred lines that can generate F1 hybrid varieties through sexual hybridization. Overcoming the gametophytic self-incompatibility through Sli is the first step in breeding at the diploid level. Then self-fertilization is performed within each breeding cycle to achieve pure diploid inbred lines. However, reaching full homozygosity is made difficult by severe inbreeding depression in potato. As a result, multiple hybridization events are needed to break linkages with the deleterious alleles. This research aims to create the germplasm and provide the data for future diploid potato breeding. We first focused on genes that were well characterized in potato: Sli and the vine maturity gene StCDF1 (Cycling DOF Factor 1). A modified backcrossing scheme using primary dihaploids of Solanum tuberosum as the recurrent parental background allowed for the selection of self-fertile F2 individuals homozygous for Sli. By integrating haplotype and quantitative trait locus (QTL) analysis, we identified and selected partially inbred lines fixed for the two favorable alleles. They were used to initiate new cycles of selection with the goal of increasing homozygosity while maintaining plant vigor, fertility, and yield. Then we sought to discover new genetic variants by genome-wide association study (GWAS) and joint linkage mapping. Two years of field trials were performed at the Hancock Agricultural Research Station (HARS), WI, using the progeny from Backcross Cycles 1 and 2 (BC1, BC2) in the years 2020 and 2021. The traits evaluated were vine maturity, tuber appearance, tuber yield, tuber size, specific gravity, chip color, and tuber sprouting. 25 significant QTL, including CDF1 and the tuber shape gene StOFP20, were identified in GWAS. Through joint linkage mapping with connected outbred F1 progeny in the 2021 field trial, we determined the three most desirable OFP20 haplotypes for round tuber shape. We further explored the potential of utilizing genomic selection for diploid potato with the two-year field trial data. The narrow-sense heritability estimates ranged from 0.41 to 0.63. Tuber yield showed the highest prediction reliability for marker-assisted genomic selection at 0.78. Both additive and dominance effects were included in the model, and dominance was most important for tuber yield, explaining 12% of the variance through heterosis. We have also discovered that, despite lower prediction accuracy, the historical tetraploid data can be used as a training population to predict traits of diploid potatoes. The prediction ability for diploids with the mixed ploidy training population ranged from 0.1 to 0.3.
Author: Felix Eugenio Enciso Rodriguez
Author: Felix Eugenio Enciso Rodriguez
Author: Jagesh Tiwari
Author: John E. Bradshaw
Author: Swarup Kumar Chakrabarti
Author: Hugo Campos
Author: Irwin Goldman
Author: Bidyut Kumar Sarmah
Author: Lin Song (Ph.D.)
Author: G. Craig Yencho
Author: Lin Song (Ph.D.)