Assembly and annotation of the Gossypium barbadense L. 'Pima-S6' genome raise questions about the chromosome structure and gene content of Gossypium barbadense genomes.

BACKGROUND: Gossypium barbadense L. Pima cotton is known for its resistance to Fusarium wilt and for producing fibers of superior quality highly prized in the textile market. We report a high-quality genome assembly and annotation of Pima-S6 cotton and its comparison at the chromosome and protein level to other ten Gossypium published genome assemblies. RESULTS: Synteny and orthogroup analyses revealed important differences on chromosome structure and annotated proteins content between our Pima-S6 and other publicly available G. barbadense assemblies, and across Gossypium assemblies in general. Detailed synteny analyses revealed chromosomal rearrangements between Pima-S6 and other Pima genomes on several chromosomes, with three major inversions in chromosomes A09, A13 and D05, raising questions about the true chromosome structure of Gossypium barbadense genomes. CONCLUSION: Analyses of the re-assembled and re-annotated genome of the close relative G. barbadense Pima 3-79 using our Pima-S6 assembly suggest that contig placement of some recent G. barbadense assemblies might have been unduly influenced by the use of the G. hirsutum TM-1 genome as the anchoring reference. The Pima-S6 reference genome provides a valuable genomic resource and offers new insights on genomic structure, and can serve as G. barbadense genome reference for future assemblies and further support FOV4-related studies and breeding efforts.

Characterization of Current Fusarium oxysporum f. sp. vasinfectum Isolates from Cotton in the San Joaquin Valley of California and Lower Valley El Paso, Texas.

Fusarium oxysporum f. sp. vasinfectum race 4 is a causal agent of Fusarium wilt of cotton (Gossypium spp.). This study aimed to characterize the existing distribution and frequency of current field populations of F. oxysporum f. sp. vasinfectum race 4 genotypes in the San Joaquin Valley (SJV) of California and Lower Valley El Paso, TX and examine representative isolates for aggressiveness during different stages of seedling development. A survey was conducted from 2017 to 2019 across 13 locations in the SJV and one location in El Paso, TX during 2018. From the SJV, isolates identified as the F. oxysporum f. sp. vasinfectum race 4 T genotype were dispersed across the SJV, whereas isolates identified as the F. oxysporum f. sp. vasinfectum race 4 N genotype were most frequently isolated from cotton fields in the northern county of Merced. The F. oxysporum f. sp. vasinfectum race 4 isolates from the Texas location were identified as the MT genotype. A selection of representative isolates was evaluated using three inoculation assays (rolled-towel, F. oxysporum f. sp. vasinfectum-infested oat seed, and root-dip inoculation) to test the isolates' abilities to produce symptoms during seedling stages of cotton development. All isolates tested were capable of producing symptoms on cotton; however, isolate aggressiveness varied within and across inoculation assays. In all assays, higher levels of disease development were observed in the moderately susceptible Pima (Gossypium barbadense L.) cultivars (DP-340 or PHY-830) when compared with the moderately tolerant Upland (G. hirsutum L.) cultivar (FM-2334). However, no correlation was found among the different response variables for the rolled-towel assay when compared with the root-dip and infested oat seed assays. These results suggest that different genes are involved in the resistance response during the early seedling development stage measured in the rolled-towel assay compared with the later seedling development stages measured during the root-dip inoculation and infested oat seed assays, revealing the complexity of the Fusarium wilt disease and host-plant resistance mechanisms.

Enhancing Upland cotton for drought resilience, productivity, and fiber quality: comparative evaluation and genetic dissection.

To provision the world sustainably, modern society must increase overall crop production, while conserving and preserving natural resources. Producing more with diminishing water resources is an especially daunting endeavor. Toward the goal of genetically improving drought resilience of cultivated Upland cotton (Gossypium hirsutum L.), this study addresses the genetics of differential yield components referred to as productivity and fiber quality traits under regular-water versus low-water (LW) field conditions. We used ten traits to assess water stress deficit, which included six productivity and four fiber quality traits on two recombinant inbred line (RIL) populations from reciprocally crossed cultivars, Phytogen 72 and Stoneville 474. To facilitate genetic inferences, we genotyped RILs with the CottonSNP63K array, assembled high-density linkage maps of over 7000 SNPs and then analyzed quantitative trait variations. Analysis of variance revealed significant differences for all traits (p < 0.05) in these RIL populations. Although the LW irrigation regime significantly reduced all traits, except lint percent, the RILs exhibited a broad phenotypic spectrum of heritable differences across the water regimes. Transgressive segregation occurred among the RILs, suggesting the possibility of genetic gain through phenotypic selection for drought resilience and perhaps through marker-based selection. Analyses revealed more than 150 quantitative trait loci (QTLs) associated with productivity and fiber quality traits (p < 0.005) on different genomic regions of the cotton genome. The multiple-QTL models analysis with LOD > 3.0 detected 21 QTLs associated with productivity and 22 QTLs associated with fiber quality. For fiber traits, strong clustering and QTL associations occurred in c08 and its homolog c24 as well as c10, c14, and c21. Using contemporary genome sequence assemblies and bioinformatically related information, the identification of genomic regions associated with responses to plant stress/drought elevates the possibility of using marker-assisted and omics-based selection to enhance breeding for drought resilient cultivars and identifying candidate genes and networks. RILs with different responses to drought indicated that it is possible to maintain high fiber quality under LW conditions or reduce the of LW impact on quality. The heritable variation among elite bi-parental RILs for productivity and quality under field drought conditions, and their association of QTLs, and thus specific genomic regions, indicate opportunities for breeding-based gains in water resource conservation, i.e., enhancing cotton's agricultural sustainability.

First report of fibropapillomatosis in an olive ridley turtle Lepidochelys olivacea from the southeastern Pacific.

An adult olive ridley turtle Lepidochelys olivacea with lesions suggestive of fibropapillomatosis was rescued on the coast of San Antonio, central Chile. Histopathologic analysis showed an exophytic and pedunculated mass formed by epidermal papillary projections supported by fibrovascular cores, epidermal hyperplasia and marked orthokeratotic hyperkeratosis. ChHV5 unique long genes UL27, UL28 and UL30 were amplified from tumor lesions and sequenced for phylogeny. Phylogenetic reconstruction showed the Chilean sequences clustering with the Eastern Pacific group. This is the first case of fibropapillomatosis in an olive ridley turtle diagnosed in Chile and in the southeastern Pacific region. Our results suggest a regional grouping of ChHV5 variants independent of the marine turtle's species.

Quantitative Trait Loci Mapping of Multiple Independent Loci for Resistance to Fusarium oxysporum f. sp. vasinfectum Races 1 and 4 in an Interspecific Cotton Population.

Fusarium wilt, caused by the soilborne fungal pathogen Fusarium oxysporum f. sp. vasinfectum, is a vascular disease of cotton (Gossypium spp.). F. oxysporum f. sp. vasinfectum race 1 (FOV1) causes major plant injury and yield loss in G. hirsutum cultivars with coinfection with root-knot nematode (Meloidogyne incognita), while F. oxysporum f. sp. vasinfectum race 4 (FOV4) causes plant damage without nematode coinfection in G. hirsutum and in G. barbadense cultivars. Quantitative trait loci (QTL) analysis of the interspecific cross G. barbadense Pima S-7 × G. hirsutum Acala NemX revealed separate multiple loci determining resistance to FOV1 and FOV4, confirming that race specificity occurs in F. oxysporum f. sp. vasinfectum. Based on the area under the disease progress stairs, six major QTLs on chromosomes (Chrs) 1, 2, 12, 15 (2), and 21 contributing 7 to 15% to FOV1 resistance and two major QTLs on Chrs 14 and 17 contributing 12 to 33% to FOV4 resistance were identified. Minor-effect QTLs contributing to resistance to both FOV1 and FOV4 were also identified. These results define and establish a pathosystem of race-specific resistance under polygenic control. This research also validates the importance of previously reported markers and chromosome regions and adds new information for the location of F. oxysporum f. sp. vasinfectum resistance genes. Some F8 recombinant inbred lines have resistance to both FOV1 and FOV4 and also to root-knot nematode, providing multiple resistance sources for breeding.

Diversity analysis of cotton (Gossypium hirsutum L.) germplasm using the CottonSNP63K Array.

BACKGROUND: Cotton germplasm resources contain beneficial alleles that can be exploited to develop germplasm adapted to emerging environmental and climate conditions. Accessions and lines have traditionally been characterized based on phenotypes, but phenotypic profiles are limited by the cost, time, and space required to make visual observations and measurements. With advances in molecular genetic methods, genotypic profiles are increasingly able to identify differences among accessions due to the larger number of genetic markers that can be measured. A combination of both methods would greatly enhance our ability to characterize germplasm resources. Recent efforts have culminated in the identification of sufficient SNP markers to establish high-throughput genotyping systems, such as the CottonSNP63K array, which enables a researcher to efficiently analyze large numbers of SNP markers and obtain highly repeatable results. In the current investigation, we have utilized the SNP array for analyzing genetic diversity primarily among cotton cultivars, making comparisons to SSR-based phylogenetic analyses, and identifying loci associated with seed nutritional traits. RESULTS: The SNP markers distinctly separated G. hirsutum from other Gossypium species and distinguished the wild from cultivated types of G. hirsutum. The markers also efficiently discerned differences among cultivars, which was the primary goal when designing the CottonSNP63K array. Population structure within the genus compared favorably with previous results obtained using SSR markers, and an association study identified loci linked to factors that affect cottonseed protein content. CONCLUSIONS: Our results provide a large genome-wide variation data set for primarily cultivated cotton. Thousands of SNPs in representative cotton genotypes provide an opportunity to finely discriminate among cultivated cotton from around the world. The SNPs will be relevant as dense markers of genome variation for association mapping approaches aimed at correlating molecular polymorphisms with variation in phenotypic traits, as well as for molecular breeding approaches in cotton.

Development, genetic mapping and QTL association of cotton PHYA, PHYB, and HY5-specific CAPS and dCAPS markers.

BACKGROUND: Among SNP markers that become increasingly valuable in molecular breeding of crop plants are the CAPS and dCAPS markers derived from the genes of interest. To date, the number of such gene-based markers is small in polyploid crop plants such as allotetraploid cotton that has A- and D-sub-genomes. The objective of this study was to develop and map new CAPS and dCAPS markers for cotton developmental-regulatory genes that are important in plant breeding programs. RESULTS: Gossypium hirsutum and G. barbadense, are the two cultivated allotetraploid cotton species. These have distinct fiber quality and other agronomic traits. Using comparative sequence analysis of characterized GSTs of the PHYA1, PHYB, and HY5 genes of G. hirsutum and G. barbadense one PHYA1-specific Mbo I/Dpn II CAPS, one PHYB-specific Alu I dCAPS, and one HY5-specific Hinf I dCAPS cotton markers were developed. These markers have successfully differentiated the two allotetraploid genomes (AD1 and AD2) when tested in parental genotypes of 'Texas Marker-1' ('TM-1'), 'Pima 3-79' and their F1 hybrids. The genetic mapping and chromosome substitution line-based deletion analyses revealed that PHYA1 gene is located in A-sub-genome chromosome 11, PHYB gene is in A-sub-genome chromosome 10, and HY5 gene is in D-sub-genome chromosome 24, on the reference 'TM-1' x 'Pima 3-79' RIL genetic map. Further, it was found that genetic linkage map regions containing phytochrome and HY5-specific markers were associated with major fiber quality and flowering time traits in previously published QTL mapping studies. CONCLUSION: This study detailed the genome mapping of three cotton phytochrome genes with newly developed CAPS and dCAPS markers. The proximity of these loci to fiber quality and other cotton QTL was demonstrated in two A-subgenome and one D-subgenome chromosomes. These candidate gene markers will be valuable for marker-assisted selection (MAS) programs to rapidly introgress G. barbadense phytochromes and/or HY5 gene (s) into G. hirsutum cotton genotypes or vice versa.

Analyses of Fusarium wilt race 3 resistance in Upland cotton (Gossypium hirsutum L.).

Fusarium wilt [Fusarium oxysporum f.sp. vasinfectum (FOV) Atk. Sny & Hans] represents a serious threat to cotton (Gossypium spp.) production. For the last few decades, the FOV pathogen has become a significant problem in Uzbekistan causing severe wilt disease and yield losses of G. hirsutum L. cultivars. We present the first genetic analyses of FOV race 3 resistance on Uzbek Cotton Germplasm with a series of field and greenhouse artificial inoculation-evaluations and inheritance studies. The field experiments were conducted in two different sites: the experimental station in Zangiota region-Environment (Env) 1 and the Institute of Cotton Breeding (Env-2, Tashkent province). The Env-1 was known to be free of FOV while the Env-2 was known to be a heavily FOV infested soil. In both (Env-1 and Env-2) of these sites, field soil was inoculated with FOV race 3. F2 and an F3 Upland populations ("Mebane B1" × "11970") were observed with a large phenotypic variance for plant survival and FOV disease severity within populations and among control or check Upland accessions. Wilt symptoms among studied F2 individuals and F3 families significantly differed depending on test type and evaluation site. Distribution of Mendelian rations of susceptible (S) and resistant (R) phenotypes were 1S:1R field Env-1 and 3S:1R field Env-2 in the F2 population, and 1S:3R greenhouse site in the F3 population. The different segregation distribution of the Uzbek populations may be explained by differences in FOV inoculum level and environmental conditions during assays. However, genetic analysis indicated a recessive single gene action under high inoculum levels or disease pressure for FOV race 3 resistance. Uzbek germplasm may be more susceptible than expected to FOV race 3, and sources of resistance to FOV may be limited under the FOV inoculum levels present in highly-infested fields making the breeding process more complex.

Mapping genomic loci for cotton plant architecture, yield components, and fiber properties in an interspecific (Gossypium hirsutum L. × G. barbadense L.) RIL population.

A quantitative trait locus (QTL) mapping was conducted to better understand the genetic control of plant architecture (PA), yield components (YC), and fiber properties (FP) in the two cultivated tetraploid species of cotton (Gossypium hirsutum L. and G. barbadense L.). One hundred and fifty-nine genomic regions were identified on a saturated genetic map of more than 2,500 SSR and SNP markers, constructed with an interspecific recombinant inbred line (RIL) population derived from the genetic standards of the respective cotton species (G. hirsutum acc. TM-1 × G. barbadense acc. 3-79). Using the single nonparametric and MQM QTL model mapping procedures, we detected 428 putative loci in the 159 genomic regions that confer 24 cotton traits in three diverse production environments [College Station F&B Road (FB), TX; Brazos Bottom (BB), TX; and Shafter (SH), CA]. These putative QTL loci included 25 loci for PA, 60 for YC, and 343 for FP, of which 3, 12, and 60, respectively, were strongly associated with the traits (LOD score ≥ 3.0). Approximately 17.7 % of the PA putative QTL, 32.9 % of the YC QTL, and 48.3 % of the FP QTL had trait associations under multiple environments. The At subgenome (chromosomes 1-13) contributed 72.7 % of loci for PA, 46.2 % for YC, and 50.4 % for FP while the Dt subgenome (chromosomes 14-26) contributed 27.3 % of loci for PA, 53.8 % for YC, and 49.6 % for FP. The data obtained from this study augment prior evidence of QTL clusters or gene islands for specific traits or biological functions existing in several non-homoeologous cotton chromosomes. DNA markers identified in the 159 genomic regions will facilitate further dissection of genetic factors underlying these important traits and marker-assisted selection in cotton.

Two de novo genome assemblies from pathogenic Fusarium oxysporum f. sp. vasinfectum race 4 (FOV4) isolates from California.

Fusarium oxysporum f. sp. vasinfectum race 4 (FOV4) is the most virulent cotton wilt pathogen in the United States. There is an urgent need for improved detection and diagnostics to combat the spread of FOV4. To help meet this challenge, we report the de novo assembly of two pathogenic isolates of FOV4 from California.

A high-quality whole-genome sequence, assembly, and gene annotation of Fusarium oxysporum f. sp. vasinfectum (Fov) race 1 from California.

Fusarium wilt [Fusarium oxysporum f. sp. vasinfectum (FOV)] in cotton is a widespread soilborne pathogen that causes vascular plant disease and is responsible for substantial crop losses worldwide. FOV race 1 (FOV1) is well established across almost all cotton production regions, especially in the USA. Herein, we report a high-quality whole-genome sequence, assembly, and gene annotation of a FOV1 isolate from California.

Lack of Highly Pathogenic Avian Influenza H5N1 in the South Shetland Islands in Antarctica, Early 2023.

In January 2023, an active surveillance initiative was undertaken in the South Shetland Islands, Antarctica, with the specific objective of ascertaining evidence for the presence of avian influenza, and specifically the highly pathogenic avian influenza virus subtype H5N1 (HPAIV H5N1). The investigation encompassed diverse locations, including Hanna Point (Livingston Island), Lions Rump (King George Island), and Base Escudero (King George Island), with targeted observations on marine mammals (southern elephant seals), flying birds (the kelp gull, snowy sheathbill and brown skua), and penguins (the chinstrap penguin and gentoo penguin). The study encompassed the examination of these sites for signs of mass mortality events possibly attributable to HPAIV H5N1, as well as sampling for influenza detection by means of real-time RT-PCR. Two hundred and seven (207) samples were collected, including 73 fecal samples obtained from the environment from marine mammals (predominantly feces of southern elephant seals), and 77 cloacal samples from penguins of the genus Pygoscelis (predominantly from the gentoo penguin). No evidence of mass mortality attributable to HPAIV H5N1 was observed, and all the collected samples tested negative for the presence of the virus, strongly suggesting the absence of the virus in the Antarctic territory during the specified period. This empirical evidence holds significant implications for both the ecological integrity of the region and the potential zoonotic threats, underscoring the importance of continued surveillance and monitoring in the Antarctic ecosystem.

Stranding and mass mortality in humboldt penguins (Spheniscus humboldti), associated to HPAIV H5N1 outbreak in Chile.

The highly pathogenic Avian Influenza virus (HPAIV) H5N1 has caused a global outbreak affecting both wild and domestic animals, predominantly avian species. To date, cases of the HPAIV H5 Clade 2.3.4.4b in penguins have exclusively been reported in African Penguins. In Chile, the virus was confirmed in pelicans in December 2022 and subsequently spread across the country, affecting several species, including Humboldt penguins. This study aims to provide an overview of the incidents involving stranded and deceased Humboldt penguins and establish a connection between these events and HPAIV H5N1. Historical data about strandings between 2009 and 2023 was collected, and samples from suspected cases in 2023 were obtained to confirm the presence of HPAIV H5N1. Between January and August 2023, 2,788 cases of stranded and deceased penguins were recorded. Out of these, a total of 2,712 penguins deceased, evidencing a significative increase in mortality starting in early 2023 coinciding with the introduction and spreading of HPAIV H5N1 in the country. Thirty-seven events were categorized as mass mortality events, with the number of deceased penguins varying from 11 to 98. Most cases (97 %) were observed in the North of Chile. One hundred and eighty-one specimens were subjected to HPAIV diagnosis, four of which tested positive for HPAIV H5N1. Spatial analysis validates the correlation between mass mortality events and outbreaks of HPAIV in Chile. However, the limited rate of HPAIV H5N1 detection, which can be attributed to the type and quality of the samples, requiring further exploration.

Inheritance and QTL mapping of Fusarium wilt race 4 resistance in cotton.

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.

Mass mortality event in South American sea lions (Otaria flavescens) correlated to highly pathogenic avian influenza (HPAI) H5N1 outbreak in Chile.

In Chile, since January 2023, a sudden and pronounced increase in strandings and mortality has been observed among South American (SA) sea lions (Otaria flavescens), prompting significant concern. Simultaneously, an outbreak of highly pathogenic avian influenza H5N1 (HPAIV H5N1) in avian species has emerged since December 2022. To investigate the cause of this unexpected mortality, we conducted a comprehensive epidemiological and pathologic study. One hundred sixty-nine SA sea lions were sampled to ascertain their HPAIV H5N1 status, and long-term stranding trends from 2009 to 2023 were analyzed. In addition, two animals were necropsied. Remarkably, a significant surge in SA sea lion strandings was observed initiating in January 2023 and peaking in June 2023, with a count of 4,545 stranded and deceased animals. Notably, this surge in mortality correlates geographically with HPAIV outbreaks affecting wild birds. Among 168 sampled SA sea lions, 34 (20%) tested positive for Influenza A virus, and 21 confirmed for HPAIV H5N1 2.3.4.4b clade in tracheal/rectal swab pools. Clinical and pathological evaluations of the two necropsied stranded sea lions revealed prevalent neurological and respiratory signs, including disorientation, tremors, ataxia, and paralysis, as well as acute dyspnea, tachypnea, profuse nasal secretion, and abdominal breathing. The lesions identified in necropsied animals aligned with observed clinical signs. Detection of the virus via immunohistochemistry (IHC) and real-time PCR in the brain and lungs affirmed the findings. The findings provide evidence between the mass mortality occurrences in SA sea lions and HPAIV, strongly indicating a causal relationship. Further studies are needed to better understand the pathogenesis and transmission.

Enhanced phenylpropanoid metabolism underlies resistance to Fusarium oxysporum f. sp. vasinfectum race 4 infection in the cotton cultivar Pima-S6 (Gossypium barbadense L.).

Introduction: Fusarium oxysporum f. sp. vasinfectum (FOV) race 4 (FOV4) is a highly pathogenic soil-borne fungus responsible for Fusarium wilt in cotton (Gossypium spp.) and represents a continuing threat to cotton production in the southwest states of the United States, including California, New Mexico, and Texas. Pima (G. barbadense L.) cotton, which is highly valued for its fiber quality, has been shown to be more susceptible to this pathogen than Upland (G. hirsutum L.) cotton. Still, some Pima cultivars present resistance to FOV4 infection. Methods: To gain insights into the FOV4-resistance mechanism, we performed comparative transcriptional and metabolomic analyses between FOV4-susceptible and FOV4-resistant Pima cotton entries. FOV4-resistant Pima-S6 and FOV4-susceptible Pima S-7 and Pima 3-79 cotton plants were infected with FOV4 in the greenhouse, and the roots harvested 11 days post-infection for further analysis. Results: We found that an enhanced root phenylpropanoid metabolism in the resistant Pima-S6 cultivar determines FOV4-resistance. Gene-ontology enrichment of phenylpropanoid biosynthesis and metabolism categories correlated with the accumulation of secondary metabolites in Pima-S6 roots. Specifically, we found esculetin, a coumarin, an inhibitor of Fusarium's growth, accumulated in the roots of Pima-S6 even under non-infected conditions. Genes related to the phenylpropanoid biosynthesis and metabolism, including phenylalanine ammonia-lyase 2 (PAL2) and pleiotropic drug resistance 12 (PDR12) transporter, were found to be upregulated in Pima-S6 roots. Discussion: Our results highlight an essential role for the phenylpropanoid synthesis pathway in FOV4 resistance in Pima-S6 cotton. These genes represent attractive research prospects for FOV4-disease resistance and breeding approaches of other cotton cultivars of economic relevance.

Cross-species transmission and PB2 mammalian adaptations of highly pathogenic avian influenza A/H5N1 viruses in Chile.

H5N1 highly pathogenic avian influenza viruses (HPAIV) emerged in wild birds in Chile in December 2022 and spilled over into poultry, marine mammals, and one human. Between December 9, 2022 - March 14, 2023, a coordinated government/academic response detected HPAIV by real-time RT-PCR in 8.5% (412/4735) of samples from 23 avian and 3 mammal orders. Whole-genome sequences obtained from 77 birds and 8 marine mammals revealed that all Chilean H5N1 viruses belong to lineage 2.3.4.4b and cluster monophyletically with viruses from Peru, indicating a single introduction from North America into Peru/Chile. Mammalian adaptations were identified in the PB2 segment: D701N in two sea lions, one human, and one shorebird, and Q591K in the human and one sea lion. Minor variant analysis revealed that D701N was present in 52.9 - 70.9% of sequence reads, indicating the presence of both genotypes within hosts. Further surveillance of spillover events is warranted to assess the emergence and potential onward transmission of mammalian adapted H5N1 HPAIV in South America.

Root-Knot Nematode Resistance in Gossypium hirsutum Determined by a Constitutive Defense-Response Transcriptional Program Avoiding a Fitness Penalty.

Cotton (Gossypium spp.) is the most important renewable source of natural textile fiber and one of the most cultivated crops around the world. Plant-parasitic nematode infestations, such as the southern Root-Knot Nematode (RKN) Meloidogyne incognita, represent a threat to cotton production worldwide. Host-plant resistance is a highly effective strategy to manage RKN; however, the underlying molecular mechanisms of RKN-resistance remain largely unknown. In this study, we harness the differences in RKN-resistance between a susceptible (Acala SJ-2, SJ2), a moderately resistant (Upland Wild Mexico Jack Jones, WMJJ), and a resistant (Acala NemX) cotton entries, to perform genome-wide comparative analysis of the root transcriptional response to M. incognita infection. RNA-seq data suggest that RKN-resistance is determined by a constitutive state of defense transcriptional behavior that prevails in the roots of the NemX cultivar. Gene ontology and protein homology analyses indicate that the root transcriptional landscape in response to RKN-infection is enriched for responses related to jasmonic and salicylic acid, two key phytohormones in plant defense responses. These responses are constitutively activated in NemX and correlate with elevated levels of these two hormones while avoiding a fitness penalty. We show that the expression of cotton genes coding for disease resistance and receptor proteins linked to RKN-resistance and perception in plants, is enhanced in the roots of RKN-resistant NemX. Members of the later gene families, located in the confidence interval of a previously identified QTL associated with RKN resistance, represent promising candidates that might facilitate introduction of RKN-resistance into valuable commercial varieties of cotton. Our study provides novel insights into the molecular mechanisms that underlie RKN resistance in cotton.

Mapping Fusarium wilt race 1 resistance genes in cotton by inheritance, QTL and sequencing composition.

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.

Sequence Composition of Bacterial Chromosome Clones in a Transgressive Root-Knot Nematode Resistance Chromosome Region in Tetraploid Cotton.

Plants evolve innate immunity including resistance genes to defend against pest and pathogen attack. Our previous studies in cotton (Gossypium spp.) revealed that one telomeric segment on chromosome (Chr) 11 in G. hirsutum cv. Acala NemX (rkn1 locus) contributed to transgressive resistance to the plant parasitic nematode Meloidogyne incognita, but the highly homologous segment on homoeologous Chr 21 had no resistance contribution. To better understand the resistance mechanism, a bacterial chromosome (BAC) library of Acala N901 (Acala NemX resistance source) was used to select, sequence, and analyze BAC clones associated with SSR markers in the complex rkn1 resistance region. Sequence alignment with the susceptible G. hirsutum cv. TM-1 genome indicated that 23 BACs mapped to TM-1-Chr11 and 18 BACs mapped to TM-1-Chr 21. Genetic and physical mapping confirmed less BAC sequence (53-84%) mapped with the TM-1 genome in the rkn1 region on Chr 11 than to the homologous region (>89%) on Chr 21. A 3.1-cM genetic distance between the rkn1 flanking markers CIR316 and CIR069 was mapped in a Pima S-7 × Acala NemX RIL population with a physical distance ∼1 Mbp in TM-1. NCBI Blast and Gene annotation indicated that both Chr 11 and Chr 21 harbor resistance gene-rich cluster regions, but more multiple homologous copies of Resistance (R) proteins and of adjacent transposable elements (TE) are present within Chr 11 than within Chr 21. (CC)-NB-LRR type R proteins were found in the rkn1 region close to CIR316, and (TIR)-NB-LRR type R proteins were identified in another resistance rich region 10 cM from CIR 316 (∼3.1 Mbp in the TM-1 genome). The identified unique insertion/deletion in NB-ARC domain, different copies of LRR domain, multiple copies or duplication of R proteins, adjacent protein kinases, or TE in the rkn1 region on Chr 11 might be major factors contributing to complex recombination and transgressive resistance.