Mapeo asociativo para caracteres de crecimiento, floración y forma del fuste en Eucalyptus cladocalyx F. Muell: 13 años en condiciones áridas

138 p.En Chile, cerca del 50% del territorio continental es considerado como árido y semiárido, y se espera que este porcentaje aumente debido al calentamiento global. Por lo tanto, resulta cada vez más importante identificar y estudiar especies capaces de tolerar estos ambientes. Eucalyptus cladocalyx es una especie que tolera ambientes con baja precipitación (< 300 mmaño-1), la cual está siendo considerada en diferentes programas de mejoramiento genético (ej. Chile, Australia), donde se ha observado variaciones significativas en características como el crecimiento, eventos de floración y la forma del fuste. Sin embargo, poco se conoce acerca de la base genética involucrada en esta variabilidad fenotípica. Considerando principalmente que: i) los marcadores moleculares microsatélites han sido transferidos con éxito entre diferentes especies de Eucalyptus, ii) el germoplasma de E. cladocalyx disponible en Chile abarca la distribución natural de la especie y iii) estudios previos han reportado significativas heredabilidades para caracteres de crecimiento, eventos de floración y forma del fuste en E. cladocalyx; en la presente tesis se formularon las siguientes hipótesis: a) una alta tasa de transferencia de marcadores microsatélites es obtenida desde el mapa consenso de Eucalyptus a E. cladocalyx, b) la diversidad genética presente en las poblaciones F1 creciendo ex situ en Chile es adecuada para estudios genéticos de asociación y para la selección asistida por marcadores, y c) a pesar de que las precipitaciones en el norte de Chile son significativamente más bajas que las encontradas en el sur de Australia, la especie E. cladocalyx mantiene los patrones de variabilidad fenotípica observados en caracteres como el crecimiento, eventos de floración y forma del fuste, los cuales permiten localizar regiones genómicas que controlan estas características mediante el uso de marcadores microsatélites. Para comprobar las hipótesis, se plantearon los siguientes objetivos: 1) evaluar la transferibilidad de marcadores microsatélites desde Eucalyptus spp. a E. cladocalyx, 2) determinar la diversidad y estructura genética en las poblaciones de E. cladocalyx establecidas en Chile y 3) analizar el desequilibrio de ligamiento y detectar asociaciones marcador- característica en E. cladocalyx mediante el uso de un modelo lineal mixto. Para ello, se utilizó un ensayo de progenie-procedencia de largo plazo (13 años) establecido en la comunidad de Tunga Norte (31°38' de latitud S, 71°19' de Longitud O; 297 msnm), localizado al sur del Desierto de Atacama en la Región de Coquimbo. El ensayo consta de cuarenta y siete familias de medios hermanos provenientes de cinco localidades australianas (procedencias), las cuales abarcan la distribución natural de la especie, y dos familias de medios hermanos provenientes de una fuente de semilla local ubicada en Illapel, Provincia de Choapa. El diseño experimental del ensayo fue de bloques completos al azar con 30 bloques y un árbol por parcela, dando un total de 1470 árboles individuales. Ciento treinta marcadores, de un total de 220 SSR evaluados, se transfirieron exitosamente desde el mapa consenso de Eucalyptus hacia E. cladocalyx, los cuales se utilizaron para genotipificar una muestra de 245 árboles, de 13 años de edad, para efectos de estudio de asociación. La heterocigosidad esperada (He) varió de 0,422 a 0,538, con una media de 0,492, indicando un moderado nivel de diversidad genética en la población evaluada, lo cual es primordial para implementar un programa de mejoramiento genético. Además, la población se dividió en tres grupos genéticamente diferenciados, los que coinciden con el patrón geográfico de las procedencias evaluadas. El desequilibrio de ligamiento declinó rápidamente de r2 = 0,391 a 0,060 en tan sólo 1 cM, y se detectó un total de 23 asociaciones significativas para los siete caracteres evaluados: floración temprana (FT), intensidad de floración (IF), capacidad reproductiva (CR), rectitud del fuste (RF), bifurcación del fuste (BF), altura del árbol (ALT) y el diámetro a la altura del pecho (DAP). La varianza fenotípica explicada por cada marcador asociado varió entre un 5,9 y 23,7% para BF y ALT, respectivamente. El marcador EMBRA101 localizado en el grupo de ligación 10 a 56,5 cM se asoció conjuntamente con DBH y ALT. Nueve marcadores SSR se asociaron con SF y STR, los que explicaron entre el 5,9 y 14,8% de la variación fenotípica. Se presenta una evaluación inicial y preliminar del grado de desequilibrio de ligamiento dentro del genoma de E. cladocalyx. Además, se reporta el primer estudio de asociación en el género Eucalyptus que considera marcadores SSR y la forma del fuste. Con todo, esta tesis entrega información novedosa y valiosa para comprender la base genética de caracteres complejos en E. cladocalyx con fines de mejoramiento genético en condiciones áridas./ABSTRACT: In Chile, about 50% of the continental territory is considered as arid and semi-arid, and this percentage is expected to increase due to global warming. Therefore, it is increasingly important to identify and study species capable of tolerating these environments. Eucalyptus cladocalyx is a species that tolerates environments with low precipitation (< 300 mmyear-1), and it is being considered in different breeding programs (e.g. Chile, Australia). Significant phenotypic variation in growth, flowering events and stem form has been reported in provenance trials. However, little is known about the genetic basis involved in this phenotypic variability. Given that, (i) microsatellite molecular markers have been successfully transferred among different species of Eucalyptus, (ii) the Germplasm of E. cladocalyx available in Chile covers the natural distribution of the species, and (iii) previous studies have found significant heritabilities for growth, flowering and stem form traits in E. cladocalyx. In the current study, the purpose is to verify the following hypotheses: (a) a high rate of transfer of microsatellite markers is obtained from the consensus map of Eucalyptus to E. cladocalyx, (b) the genetic diversity present in F1 populations growing ex situ in Chile is suitable for genetic association studies and markers assisted selection, and (c) the phenotypic variability observed in traits such as growth, flowering events and stem form in E. cladocalyx, is associated with SSR markers, which allow to identify genomic regions that control these traits in a site with significant lower precipitation than Australia's natural conditions. For that, the following objectives were proposed: 1) to evaluate the transferability of microsatellite markers from Eucalyptus spp. to E. cladocalyx, 2) to determine the diversity and genetic structure of E. cladocalyx populations established in Chile and 3) to analyze the linkage disequilibrium and detect marker-trait associations in E. cladocalyx using a mixed linear model. A long-term progeny-provenance trial (13 years) situated in the community of Tunga Norte (31° 38' latitude S, 71°19' longitude O, 297 masl), southern Atacama Desert, administrative Region of Coquimbo was used. The trial consists of 47 half-sib families of E. cladocalyx from five Australian localities (provenances) covering the natural range of the species, and two half-sib families from a local seed source (Illapel, Choapa Province). A randomized complete block design (RCBD), with 30 replicates or blocks, in singletree plots, was used (N = 1470 trees). One hundred and thirty markers, out of a total of 220 SSR evaluated, were successfully transferred from the consensus map of Eucalyptus to E. cladocalyx, which were used to genotype a sample of 245 trees, 13 years of age, for association study purposes. The expected heterozygosity (He) varied from 0.422 to 0.538, with an average of 0.492, indicating a moderate level of genetic diversity in the population evaluated, which is essential to implement a breeding program. In addition, the population was divided into three different genetic groups, which coincide with the geographical pattern of provenances studied. Linkage disequilibrium declined rapidly from r2 = 0.391 to 0.060 after only 1.0 cM, and a total of 23 significant associations were detected for the seven traits under study: early flowering (EF), flowering intensity (FI), reproductive capacity (RC), stem straightness (STR), stem forking (SF), diameter at breast height (DBH) and tree height (HT). The phenotypic variance explained by each marker-trait association varied between 5.9 and 23.7% for SF and HT, respectively. The marker EMBRA101 located on linkage group 10 at 56.5 cM was concomitantly associated with DBH and HT. Nine SSR markers were associated with SF and STR, which explain the 5.9 to 14.8% of the phenotypic variation. An initial and preliminary evaluation of the degree of linkage disequilibrium within the genome of E. cladocalyx is presented. In addition, this is the first association study of SSR markers and stem form traits in the genus Eucalyptus. Therefore, this thesis provides new and valuable information to understand the genetic basis of complex traits in E. cladocalyx, which can be useful in breeding programs in arid conditions

QTL mapping of soybean cyst nematode race 9: a generalized linear modeling approach

The Female Index (FI) is a relative measure of host suitability of a soybean line for a particular nematode population and often shows a non-normal distribution. Moreover, most quantitative trait loci (QTL) mapping methods assume that the phenotype follows a normal distribution such as composite interval mapping (CIM). Therefore, a generalized linear modeling (GLM) approach was employed to map QTL for resistance to race 9 of the soybean cyst nematode (SCN) using a total of 83 simple sequence repeat markers (SSR). Two GLM models were tested: model 1, where the FI was treated as a continuous variable, assuming a Gamma distribution with a logarithmic link function; and model 2, where the FI was treated as a categorical trait in a five-item hierarchy, assuming a multinomial distribution with a cumulative logit link function. The FI data of 108 recombinant inbred lines (RIL) confirmed the non-normal distribution for race 9 of the SCN (Shapiro-Wilk?s w=0.86, P<0.0001, skewness=1.52 and kurtosis=2.93). Eight RIL were confirmed to be resistant (FI≤10), and 23 to be highly susceptible (FI≥100). Both GLM models identified one QTL for SCN on the molecular linkage group G, between the markers Satt275 and Satt038 at 48.4 centiMorgans (P=0.017 and 0.033, for models 1 and 2, respectively). Additionally, these results were also compared with the CIM and Bayesian interval mapping (BIM) methods, assuming experimental data with a non-normal response, to determine the robustness and statistical power of these two methods for mapping QTLs. The results make clear that generalized linear modeling approach can be used as an efficient method to map QTLs in a continuous trait with a non-Gaussian distribution. CIM and BIM were robust enough for a reliable mapping of QTLs underlying nonnormally distributed data.Fil: Arriagada, Osvin. Universidad de Talca; ChileFil: Ferreira, Marcia F. S.. Universidade Federal Do Espirito Santo; BrasilFil: Cervigni, Gerardo Domingo Lucio. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Rosario. Centro de Estudios Fotosintéticos y Bioquímicos (i); ArgentinaFil: Schuster, Ivan. Central Cooperative for Agricultural Research; BrasilFil: Scapim, Carlos A.. Universidade Estadual de Maringá; BrasilFil: Mora, Freddy. Universidad de Talca; Chil

Molecular Mapping and Genomics of Grain Yield in Durum Wheat: A Review

Durum wheat is the most relevant cereal for the whole of Mediterranean agriculture, due to its intrinsic adaptation to dryland and semi-arid environments and to its strong historical cultivation tradition. It is not only relevant for the primary production sector, but also for the food industry chains associated with it. In Mediterranean environments, wheat is mostly grown under rainfed conditions and the crop is frequently exposed to environmental stresses, with high temperatures and water scarcity especially during the grain filling period. For these reasons, and due to recurrent disease epidemics, Mediterranean wheat productivity often remains under potential levels. Many studies, using both linkage analysis (LA) and a genome-wide association study (GWAS), have identified the genomic regions controlling the grain yield and the associated markers that can be used for marker-assisted selection (MAS) programs. Here, we have summarized all the current studies identifying quantitative trait loci (QTLs) and/or candidate genes involved in the main traits linked to grain yield: kernel weight, number of kernels per spike and number of spikes per unit area

Identification of QTL underlying agronomic, morphological and physiological traits in barley under rainfed conditions using SNP markers

Barley (Hordeum vulgare L.) is considered a good genetic model for evaluating mechanisms of drought tolerance, and it is the most important threat to crop production worldwide. This study aimed to identify single-nucleotide polymorphisms (SNPs) associated with agronomic, morphological and physiological traits in a population of 137 recombinant chromosome substitution lines (RCSL) of barley, which were evaluated under rainfed conditions, in Cauquenes, southern Chile (35°58’ S, 72°17’ W). The annual precipitation was 299 mm during the growing season. Fifty-two significant QTLs were detected for the studied traits, which explained between 5% and 13.8% of the phenotypic variation. A genomic region on chromosome 1H (that comprises SNPs 2711-234 and 1923-265) accounted for 13.4% and 13.8%, respectively, of the grain yield variation. In addition, SNPs 8388-578 and 7639-122 on the chromosome 5H had a moderate effect, explaining 12.8% of the plant height variation. Moreover, some SNPs were associated with more than one trait, and clusters of QTLs for yield and related traits were also found. Finally, the QTLs identified in the present study are of particular interest for barley-breeding purposes under rainfed conditions.

A Comprehensive Review on Chickpea (Cicer arietinum L.) Breeding for Abiotic Stress Tolerance and Climate Change Resilience

Chickpea is one of the most important pulse crops worldwide, being an excellent source of protein. It is grown under rain-fed conditions averaging yields of 1 t/ha, far from its potential of 6 t/ha under optimum conditions. The combined effects of heat, cold, drought, and salinity affect species productivity. In this regard, several physiological, biochemical, and molecular mechanisms are reviewed to confer tolerance to abiotic stress. A large collection of nearly 100,000 chickpea accessions is the basis of breeding programs, and important advances have been achieved through conventional breeding, such as germplasm introduction, gene/allele introgression, and mutagenesis. In parallel, advances in molecular biology and high-throughput sequencing have allowed the development of specific molecular markers for the genus Cicer, facilitating marker-assisted selection for yield components and abiotic tolerance. Further, transcriptomics, proteomics, and metabolomics have permitted the identification of specific genes, proteins, and metabolites associated with tolerance to abiotic stress of chickpea. Furthermore, some promising results have been obtained in studies with transgenic plants and with the use of gene editing to obtain drought-tolerant chickpea. Finally, we propose some future lines of research that may be useful to obtain chickpea genotypes tolerant to abiotic stress in a scenario of climate change

Meta-QTL Analysis for Yield Components in Common Bean (<i>Phaseolus vulgaris</i> L.)

Common bean is one of the most important legumes produced and consumed worldwide because it is a highly valuable food for the human diet. However, its production is mainly carried out by small farmers, who obtain average grain yields below the potential yield of the species. In this sense, numerous mapping studies have been conducted to identify quantitative trait loci (QTL) associated with yield components in common bean. Meta-QTL (MQTL) analysis is a useful approach to combine data sets and for creating consensus positions for the QTL detected in independent studies. Consequently, the objective of this study was to perform a MQTL analysis to identify the most reliable and stable genomic regions associated with yield-related traits of common bean. A total of 667 QTL associated with yield-related traits reported in 21 different studies were collected. A total of 42 MQTL associated with yield-related traits were identified, in which the average confidence interval (CI) of the MQTL was 3.41 times lower than the CIs of the original QTL. Most of the MQTL (28) identified in this study contain QTL associated with yield and phenological traits; therefore, these MQTL can be useful in common bean breeding programs. Finally, a total of 18 candidate genes were identified and associated with grain yield within these MQTL, with functions related to ubiquitin ligase complex, response to auxin, and translation elongation factor activity

Comparison of durum with ancient tetraploid wheats from an agronomical, chemical, nutritional, and genetic standpoints: a review

Under intense breeding, modern wheats, such as durum (Triticum turgidum L. ssp. durum), are believed to have lost nutritional quality and protein content while increasing productivity. Emmer (Triticum turgidum ssp. dicoccum Thell) and wild emmer (Triticum turgidum ssp. dicoccoides) are alternative resources for breeding programs by offering favorable alleles to be introgressed into modern materials and thus broadening their genetic diversity. Studies conducted so far have shown that durum wheat has better performance in agronomical qualities and protein quality than T. dicoccum and T. dicoccoides. However, its grain protein content (GPC) and Fe/Zn concentrations are lower. Several QTL for yield, GPC, and nutrient content in T. dicoccoides have been described, demonstrating its potential for transfer of important genes such as Gpc-B1 into modern cultivars. The Gpc-B1 gene increased the grain protein and Fe and Zn contents, but the agronomic performance of some of the modern recipients was reduced. Understanding the correlations and relationships between agronomic, chemical, and nutritional qualities would simplify selection through breeding for a single trait. Combining this knowledge with conventional breeding, MAS, and new breeding techniques would facilitate the QTL studies in these ancestral wheats and the development of new durum cultivars while retaining the agronomic qualities. In this review, we compare some grain parameters of T. durum, T. dicoccum, and T. dicoccoides wheats, including Fe and Zn content and their genetic aspects, and the existing information is analyzed and integrated for the future prospects of durum wheat improvement