Winterhardiness in cereals is the consequence of a number of complex and interacting component characters: cold tolerance, vernalization requirement, and photoperiod sensitivity. An understanding of the genetic basis of these component traits should allow for more-effective selection. Genome map-based analyses hold considerable promise for dissecting complex phenotypes. A 74-point linkage map was developed from 100 doubled haploid lines derived from a winter x spring barley cross and used as the basis for quantitative trait locus (QTL) analyses to determine the chromosome location of genes controlling components of winterhardiness. Despite the greater genome coverage provided by the current map, a previously-reported interval on chromosome 7 remains the only region where significant QTL effects for winter survival were detected in this population. QTLs for growth habit and heading date, under 16 h and 24 h light, map to the same region. A QTL for heading date under these photoperiod regimes also maps to chromosome 2. Contrasting alleles at these loci interact in an epistatic fashion. A distinct set of QTLs mapping to chromosomes 1, 2, 3, and 5 determined heading date under 8 h of light. Under field conditions, all QTLs identified under controlled environment conditions were determinants of heading date. Patterns of differential QTL expression, coupled with additive and additive x additive QTL effects, underscore the complexity of winterhardiness. The presence of unique phenotype combinations in the mapping population suggests that coincident QTLs for heading date and winter survival represent the effects of linkage rather than pleiotropy.
Diseases such as Fusarium wilt [Fusarium oxysporum f.sp. vasinfectum (FOV) Atk. Sny & Hans] represent expanding threats to cotton production. Integrating disease resistance into high-yielding, high-fiber quality cotton (Gossypium spp.) cultivars is one of the most important objectives in cotton breeding programs worldwide. In this study, we conducted a comprehensive analysis of gene action in cotton governing FOV race 4 resistance by combining conventional inheritance and quantitative trait loci (QTL) mapping with molecular markers. A set of diverse cotton populations was generated from crosses encompassing multiple genetic backgrounds. FOV race 4 resistance was investigated using seven parents and their derived populations: three intraspecific (G. hirsutum × G. hirsutum L. and G. barbadense × G. barbadense L.) F1 and F2; five interspecific (G. hirsutum × G. barbadense) F1 and F2; and one RIL. Parents and populations were evaluated for disease severity index (DSI) of leaves, and vascular stem and root staining (VRS) in four greenhouse and two field experiments. Initially, a single resistance gene (Fov4) model was observed in F2 populations based on inheritance of phenotypes. This single Fov4 gene had a major dominant gene action and conferred resistance to FOV race 4 in Pima-S6. The Fov4 gene appears to be located near a genome region on chromosome 14 marked with a QTL Fov4-C14 1 , which made the biggest contribution to the FOV race 4 resistance of the generated F2 progeny. Additional genetic and QTL analyses also identified a set of 11 SSR markers that indicated the involvement of more than one gene and gene interactions across six linkage groups/chromosomes (3, 6, 8, 14, 17, and 25) in the inheritance of FOV race 4 resistance. QTLs detected with minor effects in these populations explained 5-19 % of the DSI or VRS variation. Identified SSR markers for the resistance QTLs with major and minor effects will facilitate for the first time marker-assisted selection for the introgression of FOV race 4 resistance into elite cultivars during the breeding process.
Recent increases in glyphosate use in perennial crops of California, USA, are hypothesized to have led to an increase in selection and evolution of resistance to the herbicide in Conyza canadensis populations. To gain insight into the evolutionary origins and spread of resistance and to inform glyphosate resistance management strategies, we investigated the geographical distribution of glyphosate resistance in C. canadensis across and surrounding the Central Valley, its spatial relationship to groundwater protection areas (GWPA), and the genetic diversity and population structure and history using microsatellite markers. Frequencies of resistant individuals in 42 sampled populations were positively correlated with the size of GWPA within counties. Analyses of population genetic structure also supported spread of resistance in these areas. Bayesian clustering and approximate Bayesian computation (ABC) analyses revealed multiple independent origins of resistance within the Central Valley. Based on parameter estimation in the ABC analyses, resistant genotypes underwent expansion after glyphosate use began in agriculture, but many years before it was detected. Thus, diversity in weed control practices prior to herbicide regulation in GWPA probably kept resistance frequencies low. Regionally coordinated efforts to reduce seed dispersal and selection pressure are needed to manage glyphosate resistance in C. canadensis.
Knowledge of the inheritance of disease resistance and genomic regions housing resistance (R) genes is essential to prevent expanding pathogen threats such as Fusarium wilt [Fusarium oxysporum f.sp. vasinfectum (FOV) Atk. Sny & Hans] in cotton (Gossypium spp.). We conducted a comprehensive study combining conventional inheritance, genetic and quantitative trait loci (QTL) mapping, QTL marker-sequence composition, and genome sequencing to examine the distribution, structure and organization of disease R genes to race 1 of FOV in the cotton genome. Molecular markers were applied to F(2) and recombinant inbred line (RIL) interspecific mapping populations from the crosses Pima-S7 (G. barbadense L.) × 'Acala NemX' (G. hirsutum L.) and Upland TM-1 (G. hirsutum) × Pima 3-79 (G. barbadense), respectively. Three greenhouse tests and one field test were used to obtain sequential estimates of severity index (DSI) of leaves, and vascular stem and root staining (VRS). A single resistance gene model was observed for the F(2) population based on inheritance of phenotypes. However, additional inheritance analyses and QTL mapping indicated gene interactions and inheritance from nine cotton chromosomes, with major QTLs detected on five chromosomes [Fov1-C06, Fov1-C08, (Fov1-C11 ( 1 ) and Fov1-C11 ( 2)) , Fov1-C16 and Fov1-C19 loci], explaining 8-31% of the DSI or VRS variation. The Fov1-C16 QTL locus identified in the F(2) and in the RIL populations had a significant role in conferring FOV race 1 resistance in different cotton backgrounds. Identified molecular markers may have important potential for breeding effective FOV race 1 resistance into elite cultivars by marker-assisted selection. Reconciliation between genetic and physical mapping of gene annotations from marker-DNA and new DNA sequences of BAC clones tagged with the resistance-associated QTLs revealed defenses genes induced upon pathogen infection and gene regions rich in disease-response elements, respectively. These offer candidate gene targets for Fusarium wilt resistance response in cotton and other host plants.
During the past 9 yr, a new race of Fusarium (Fusarium oxysporum f. sp. vasinfectum [FOV Race 4]) has increasingly impacted cotton (Gossypium spp.) in the San Joaquin Valley of California. To assess the vulnerability of upland cotton (G. hirsutum L.) in California to FOV disease, elite upland germplasm lines from 13 U.S. public breeding programs across the Cotton Belt and commercial cultivars were evaluated for disease resistance to FOV Races 1 and 4. Ten independent replicated field trials were conducted: three in 2008, four in 2010, and three in 2011. Significant differences (P ≤ 0.05) were observed for disease severity index of leaves, vascular root staining, and plant survival values among the elite germplasm lines in all 3 yr for the levels of resistance–response to FOV Races 1 and 4. Also, significant interactions among germplasm lines, FOV races (1 and 4), and evaluation sites indicated that germplasm lines differed in mechanisms of plant‐defense response for the two FOV races. Selected lines from programs in the states of Alabama, Arkansas, Louisiana, and Mississippi showed at least a moderate level of tolerance to both FOV races; however, several of these lines produced weak and coarse fibers. Based on these evaluations, many of the entries in public breeders’ current elite upland germplasm pools may be more susceptible than expected to some FOV races, and sources of acceptable levels of resistance may be limited when tested under infestation levels that resulted in only 5 to 35% plant survival in susceptible check cultivars.
Four Pima cotton (Gossypium barbadense L.) germplasm lines, SJ‐07P‐FR01 (Reg. No. GP‐910, PI 654065), SJ‐07P‐FR02 (Reg. No. GP‐911, PI 654066), SJ‐07P‐FR03 (Reg. No. GP‐912, PI 654067), and SJ‐07P‐FR04 (Reg. No. GP‐913, PI 654068), were developed by the USDA–ARS and New Mexico State University Agricultural Experiment Station and jointly released with the University of California in 2008. The primary purpose for these releases is to provide germplasm with good levels of resistance to Fusarium wilt [Fusarium oxysporum f. sp. vasinfectum Atk. Sny & Hans] (FOV) race 4 to cotton breeders in California. Lines SJ‐07P‐FR01 to ‐FR03 originated from a cross made at New Mexico State University in 1997 of germplasm lines 8810 and NMSI 1601. The germplasm line SJ‐07P‐FR04 originated from reselection within the publicly released USDA–ARS germplasm line P 73. The lines were evaluated for resistance to race 4 in two field and three greenhouse trials conducted in 2003 and 2005. Five replicated field evaluations for yield potential, fiber characteristics, and other agronomic traits were conducted at Five Points, CA, Shafter, CA, and Maricopa, AZ, in 2005 and 2006. The SJ‐07P‐FR series possesses good resistance, moderate lint yield potential, and good to superior fiber length and strength. Caution should be applied when using these lines, and it should not be assumed that the lines provide complete resistance against FOV race 4.
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