Genetic Characterization of the Pee Dee Cotton Breeding Program

The history of cotton breeding in the southeastern United States is multifaceted and complex. Public and private breeding programs have driven cotton’s genetic development over the past two centuries. The Pee Dee breeding program in Florence, South Carolina, has had a substantial role in the development of well-adapted cotton cultivars with improved fiber strength, fiber length, and performance in farmers’ fields. Despite the historic importance of the cotton germplasm lines and varieties from the Pee Dee program, little has been done to characterize the population structure and genetic architecture of key traits in this closed breeding program. Here, I first provide an in-depth exploration of the rich history of cotton breeding and genetics over the past century to provide some context for the remainder of this thesis. Then, I discuss the interface of breeding goals, population genetics, and historical implications of a representative sample across 85+ years of cotton breeding in the Pee Dee program. Once the family structure had been evaluated, I applied modern statistical methodology to find gene haplotypes that are associated with improved fiber quality or field performance and attempted to trace the origin of some beneficial alleles. Lastly, I talk about the implications of our work and how it may influence future breeding efforts to utilize the germplasm from this diverse cotton collection

Establecimiento de las bases genéticas para la mejora del algodón en el Valle del Guadalquivir

El algodón (Gossypium spp.) sigue siendo en la actualidad la principal fuente de fibra de origen natural a nivel mundial, y es uno de los cultivos que más enriquece a la población rural por la alta mano de obra demandada en todo el proceso industrial de la fibra (producción, desmotación, hilatura, tejidos, confección y distribución). Dentro de la Unión Europea, el algodón tiene un papel fundamental en el gran mercado de la moda, pero especialmente a nivel social para los dos únicos Estados productores, Grecia y España, con el 79% y el 21% de la superficie cultivada respectivamente. En estas regiones el algodón y su industria asociada generan más empleo y beneficios que ningún otro cultivo alternativo. Sin embargo, numerosos motivos políticos, bursátiles y de competencia con otras fibras han provocado en los últimos años una gran incertidumbre en el sector algodonero europeo. En España, casi el 100% del algodón se cultiva en Andalucía (principalmente en las provincias de Sevilla y Cádiz), abarcando una superficie en la actualidad de 68,000 ha y la mayoría de regadío. Dadas las peculiaridades climáticas y el riguroso manejo que acontecen en esta zona, la mejora varietal del algodón se presenta como una de las soluciones más sonadas. Por tanto existe la necesidad de ampliar el catálogo de variedades europeas, buscando una mayor sostenibilidad y calidad de la fibra, pero también una mejor adaptación de los ciclos y el vigor de las futuras variedades. El 95% de la producción mundial de algodón corresponde a la especie Gossypium hirsutum (Upland) que ofrece grandes producciones y buena adaptabilidad, pero una aceptable calidad de fibra (categoría “larga”). Sin embargo, la diversidad genética dentro de estas variedades Upland comerciales es baja, y la uniformidad genética está suponiendo muchos obstáculos a los mejoradores. La segunda especie cultivada a nivel mundial es G. barbadense (Pima), elegida por su Fibra Extra Larga (ELS) altamente demandada aunque su producción suele ser menor. En Andalucía, las variedades Pima no encajan dado el largo ciclo que poseen y en los últimos años, la empresa Algodonera del Sur S.A., ha estado apostando por los híbridos interespecíficos (G. hirsutum × G. barbadense) comerciales, que pese a su excesivo vigor para nuestras condiciones climáticas, prometen ser la respuesta a las necesidades del sector. Es en este punto donde surge el proyecto de la presente tesis, al comprobar que apenas había información fenotípica y molecular para apoyar a la mejora del algodón europeo, tanto de nuevas variedades Upland como de híbridos ELS mejor adaptados. Por tanto, el primer objetivo de este trabajo consistió en la selección y caracterización de una colección de 48 variedades comerciales y experimentales de algodón (sobre todo Upland y Pima) con potencial para la mejora. Mediante el uso de una batería de 67 marcadores microsatélites (SSR), un posterior estudio de la filogenia y la toma de datos de campo sobre caracteres morfológicos, de potencial productivo y de calidad de la fibra, pudo constatarse la importante diversidad genética y fenotípica contenida en esta colección vegetal, tanto inter como intra especie. Algunas variedades resultaron interesantes como parental donante de ciertos caracteres (Ej.: Fantom o WC-19NSSL) o fondo genético recurrente (Ej.: Elpida, TM-1, Campo o GW-4269) para futuros procesos de selección y mejora. Los resultados anteriores, además sirvieron para guiar el segundo objetivo de esta tesis: iniciar un programa de cruzamientos para la futura obtención de híbridos ELS con menor vigor que los testigos comerciales Intercott-211 e Intercott-670. Aunque la aptitud combinatoria específica (ACE) ha sido menos importante que la aptitud combinatoria general (ACG) en la caracterización fenotípica de las 19 combinaciones experimentales de híbridos, se mostró que es posible obtener híbridos mejor adaptados que los testigos a las condiciones de cultivo de Andalucía (menor vigor, ciclos más cortos y buen rendimiento). La variedad Lider (Upland) ha mostrado ser el parental femenino con mejor ACG, pues sus descendencias han mostrado generalmente un menor vigor, ciclos más cortos y buenos rendimientos debido al gran número y peso de los frutos, en comparación con los testigos comerciales. Así que la variedad Lider habría que tenerla en cuenta en nuevas combinaciones híbridas, además de realizar nuevas evaluaciones de estos y otros híbridos en diferentes años o localidades para confirmar los resultados de esta tesis. En conclusión, la mejora genética de nuevas variedades de algodón Upland adaptadas a las condiciones de cultivo europeas, aumentaría la productividad, mejoraría el precio de la fibra, y además en el caso de nuevos híbridos ELS, el precio de la fibra sería mayor por defecto y además se reducirían las pérdidas económicas derivadas de la falta de agua y las plagas, dada la mayor tolerancia y resistencia de los híbridos ante los distintos estreses ambientales. Por tanto, la mejora varietal permitiría un aumento de la rentabilidad del cultivo, y una mejora de la competitividad y sostenibilidad del sector algodonero.Cotton (Gossypium spp.) is still the main source of natural fiber worldwide, and is one of the crops that most enriches the rural population due to its high labor demand along the entire industrial process of the fiber (production, ginning, spinning, weaving, confection and distribution). Within the European Union, cotton has a fundamental role in the large fashion market, but especially in the social level for the two producer countries, Greece and Spain, with 79% and 21% of the cultivated area respectively. In these regions, cotton crop and its associated industry generate more employment and benefits than any other alternative crop. However, several political, stock market and competition with other fibers reasons have caused in recent years a great uncertainty in the European cotton sector. In Spain, almost 100% of the cotton is grown in Andalusia (mainly in the provinces of Seville and Cadiz), covering an area of 68,000 ha, mostly irrigated. Given the climatic peculiarities and the rigorous management that occurs in this area, the improvement of the cotton varieties is presented as one of the most talked about solutions. Therefore there is a need to expand the catalogue of European varieties, seeking greater sustainability and fiber quality, but also a better adaptation of the cycles and the vigor of future varieties. 95% of the world cotton production corresponds to the species Gossypium hirsutum (Upland) that offers large productions and good adaptability, but an acceptable fiber quality ("long" category). However, the genetic diversity within these commercial Upland varieties is low, and genetic uniformity is posing many obstacles to breeders. The second species cultivated worldwide is G. barbadense (Pima), chosen for its highly demanded Extra Long Staple (ELS) although its production is usually lower. In Andalusian climatic conditions, Pima varieties do not fit well given the long cycle they have. In recent years, the company Algodonera del Sur S.A., has been wagered on commercial interspecific hybrids (G. hirsutum × G. barbadense) whose promise to be the answer to the needs of the sector, despite its excessive vigor for our climatic conditions. It is at this point where the project of the present thesis arises, when checking that there was a scarcity of phenotypic and molecular information to support the improvement of European cotton, both new Upland varieties and better adapted ELS hybrids. Therefore, the first objective of this work consisted in the selection and characterization of a cotton collection of 48 commercial and experimental varieties with potential for improvement (especially Upland and Pima). Through the use of 67 microsatellite markers (SSR), a subsequent study of the phylogeny and the taking of field data on morphological characters, productive potential and fiber quality, we found an important genetic and phenotypic diversity contained in this vegetal collection, both inter and intra species. Some varieties were interesting as a donor parent of certain characters (e.g.: Fantom or WC-19NSSL) or as recurrent genetic background (e.g.: Elpida, TM-1, Campo or GW-4269) for future selection and improvement processes. The previous results also served to guide the second objective of this thesis: to initiate a crossings program for the future obtaining of ELS hybrids with less vigor than the commercial witnesses Intercott-211 and Intercott-670. Although in the phenotypic characterization of the 19 experimental combinations of hybrids the specific combining ability (SCA) has been less important than the general combining ability (GCA), it was shown that it is possible to obtain better adapted hybrids than the controls to the Andalusian climatic conditions (less vigor, shorter cycles and good performance). Lider variety (Upland) has been shown to be the female parent with the best GCA, as its offspring have generally shown lower vigor, shorter cycles and good yields due to the large number and weight of their fruits, compared to commercial controls. So Lider variety should be taken into account in new hybrid combinations, in addition to making new assessments of these and other hybrids in different years or locations to confirm the results of this thesis. In conclusion, the genetic improvement of new varieties of Upland cotton adapted to European farming conditions, would increase productivity, improve the price of fiber, and also in the case of new ELS hybrids, would reduce economic losses resulting from the lack of water and pests attacks, given the greater tolerance and resistance of the hybrids to different environmental stresses. Therefore, the varietal improvement would allow an increase in crop profitability, and a better competitiveness and sustainability of the cotton sector

Genetic variation and genome-environment association of alfalfa (Medicago sativa L.) populations under long-term grazing

Alfalfa (Medicago sativa. L) is the most valuable forage legume for the beef, dairy, and forage industries in Canada with approximately 4 million hectares of alfalfa and alfalfa-grass mixtures in Western Canada. Alfalfa forage production has been limited by low stand persistence due to the negative impacts of environmental factors and continuous grazing. The objectives of this study were: 1) to identify the phenotypic and genetic diversities of alfalfa populations collected from long-term grazing sites across four soil zones of Saskatchewan; 2) to compare genetic structure of the populations from long-term grazing sites to commercial alfalfa cultivars released between 1926 and 1980; 3) to identify the SNP markers linked to morphological traits and nutritive values; and 4) to detect SNP markers associated with environmental factors associated with plant persistence at long-term grazing sites. This study collected alfalfa populations across four soil zones of Saskatchewan representing 14 alfalfa stands with minimum 25 years of grazing history. The seven agro-morphological and three nutritive value traits of the 14 alfalfa populations from long-term grazing were evaluated in a replicated field trial using a nested randomized complete block design (RCBD). The genotyping-by-sequencing (GBS) reads were aligned to the Medicago sativa reference genome and 19,853 high-quality SNPs were generated. The STRUCTURE analysis identified that the alfalfa populations from long-term grazing sites were the hybrid cross from subspecies Medicago sativa subsp. sativa (hereafter M. sativa) and M. falcata. Plants from the Black soil zone produced the highest forage dry matter yield, plant height, and stem number, while the lowest values for these traits were recorded plants from the Brown soil zone. This was because the alfalfa populations from the Black soil zone had maintained more of the M. sativa genome over long-term grazing, while the alfalfa populations from the Brown soil zone maintained more of the M. falcata genome. The genotype-environment association (GEA) identified 70 SNPs for the alfalfa populations with grazing history including summer extreme temperature (22 SNPs), growing season precipitation (15 SNPs), soil nutrient (30 SNPs), and soil pH (3 SNPs). Fifty-three candidate genes were significantly associated with eight environmental factors, which were mainly involved in plant resistances to biotic and abiotic stresses, such as heat, drought, salt and diseases. The genome-wide-association-study (GWAS) analysis identified nine SNPs associated with stem number and nutritive value on the Medicago sativa reference genome. Once validated, these markers and candidate genes identified in the study would be useful for developing markers for marker-assisted selection to improve alfalfa cultivars with enhanced tolerance to long-term grazing and environmental stresses in Western Canada

Regional association analysis-based fine mapping of three clustered QTL for verticillium wilt resistance in cotton (G. hirsutum. L)

Abstract Background Verticillium wilt is one of the most destructive diseases affecting global cotton production. The most effective way to control wilt disease has been the development of new cotton varieties that are resistant to VW. VW-resistant Upland cotton cultivars have been created in both the USA and China by Gossypium barbadense introgression. More than 100 VW resistance quantitative trait loci have been detected. Results Three clustered VW resistance-related QTL were detected in a 120-line association population and assigned to a genome region of 14,653,469–55,190,112 bp in Dt_chr9. A regional association analysis-based fine-mapping strategy was developed to narrow down the confidence intervals of the above QTL. The estimated LD decay of the genome region of interest was much faster than those of the Dt_chr9 chromosome and the whole genome, suggesting the existence of a recombination hotspot. Thirty-seven haplotype blocks were detected. The confidence intervals of the three clustered QTL were narrowed down to a region of 937,906 bp involving QTL-i23734Gh and a region of 1,389,417 bp involving QTL- i10740Gh, respectively. Each region contained the strongest association signal. Comparative analysis redefined the confidence intervals of the other three QTLs, qDL52T2-c19, QTL-BNL4069, and QTL-JESPR0001. The broad-spectrum VW resistance QTL qVW-D9–1 was demonstrated to be closely linked with the three redefined QTL, QTL-i23734Gh, QTL- i10740Gh and QTL-JESPR0001. Twelve functional genes were detected to be located within the redefined confidence intervals of VW resistance QTL. The mRNA CotAD_60243, encoding E3 ubiquitin-protein ligase UPL2-like, responsible for plant innate immunity and broad-spectrum disease resistance, was found to be overlapped with the strongest association signal i10740Gh. Six mRNAs encoding putative disease-resistance proteins were within the redefined confidence interval of QTL-JESPR0001, suggesting a tandem arrangement of R genes. Conclusions Our results proved that the VW resistance effect related to three clustered VW resistance-related QTL was actually controled by two redefined major QTL and severlal minor loci. The broad-spectrum VW resistance QTL qVW-D9–1 may be closely linked with the two redefined major QTLs. The tandem arrangement of R genes were detected in the redefined confidence interval of QTL-JESPR0001. The candidate genes obtained should be helpful in identifying and characterizing defense genes related to VW resistance QTL

Genetic Diversity Assessment and Marker-Assisted Selection in Crops

The exploitation of biodiversity is essential to select resilient genotypes for sustainable cropping systems as one of the main challenges for plant breeding. Mapping traits of agronomic interest in specific genomic regions appears as another pivotal effort for the future development of novel cultivars. For this purpose, there is evidence that MAGIC and other exotic populations will play a major role in the coming years in allowing for impressive gains in plant breeding for developing new generations of improved cultivars. This Special Issue focused on the application of advanced technologies devoted to crop improvement and exploit the available biodiversity in crops. In detail, next-generation sequencing (NGS) technologies supported the development of high-density genotyping arrays for different plants included in this issue

Translational Genomics for Crop Breeding: Biotic Stress, Volume 1

Genomic Applications for Crop Breeding: Biotic Stress is the first of two volumes looking at the latest advances in genomic applications to crop breeding. This volume focuses on genomic-assisted advances for improving economically important crops against biotic stressors, such as viruses, fungi, nematodes, and bacteria. Looking at key advances in crops such as rice, barley, wheat, and potato amongst others, Genomic Applications for Crop Breeding: Biotic Stress will be an essential reference for crop scientists, geneticists, breeders, industry personnel and advanced students in the field

Additional file 2: Table S2. of Regional association analysis-based fine mapping of three clustered QTL for verticillium wilt resistance in cotton (G. hirsutum. L)

Physical position of verticillium wilt resistance-related QTL or markers. (XLSX 12 kb

Advances in Molecular Breeding of Vegetable Crops

Vegetable crops provide valuable minerals and vitamins that are indispensible for human health. Scientists have been working on the genetics of vegetable crops, deciphering the molecular bases of agronomically important traits. These genetic bases and variations in vegetable traits will greatly facilitate vegetable genetic improvement. Therefore, the genes of and genetic research on vegetable crops are of great importance. This Special Issue is a collection of 13 important research papers addressing the genes, genetics, and breeding of major vegetable crops. In the present book, the authors described the genes and QTLs responsible for stress tolerance, disease resistance, vegetable yield, and quality. The 13 research papers cover germplasm enhancement and evaluation, QTL mapping, gene isolation, marker development, and gene expression as well as gene editing in a wide range of vegetable species, including broccoli, pepper, eggplant, onion, and Cucurbita species. Readers from all over the globe are expected to greatly benefit from this Special Issue collection regarding their own work and the goal of improving breeding efficiency with molecular breeding to generate environment-adaptive, high-yield, and high-quality vegetable crops with which to feed the global population of 9.7 billion in an extreme climate by 2050

Integrated nematode management

This book outlines the economic importance of specific plant parasitic nematode problems on the major food and industrial crops and presents the state-of-the-art management strategies that have been developed to reduce specific nematode impacts and outlines their limitations. Case studies to illustrate nematode impact in the field are presented and future changes in nematode disease pressure that might develop as a result of climate change and new cropping systems are discussed.illustrato