A computational model of evolution: haploidy versus diploidy

In this paper, the study of diploidy is introduced like and important mechanism for memory reinforcement in artificial environments where adaptation is very important. The individuals of this ecosystem are able to genetically "learn" the best behaviour for survival. Critical changes, happening in the environmental conditions, require the presence of diploidy to ensure the survival of species. By means of new gene-dominance configurations, a way to shield the individuals from erroneous selection is provided. These two concepts appear like important elements for artificial systems which have to evolve in environments with some degree of instability.Publicad

Adaptive primal-dual genetic algorithms in dynamic environments

This article is placed here with permission of IEEE - Copyright @ 2010 IEEERecently, there has been an increasing interest in applying genetic algorithms (GAs) in dynamic environments. Inspired by the complementary and dominance mechanisms in nature, a primal-dual GA (PDGA) has been proposed for dynamic optimization problems (DOPs). In this paper, an important operator in PDGA, i.e., the primal-dual mapping (PDM) scheme, is further investigated to improve the robustness and adaptability of PDGA in dynamic environments. In the improved scheme, two different probability-based PDM operators, where the mapping probability of each allele in the chromosome string is calculated through the statistical information of the distribution of alleles in the corresponding gene locus over the population, are effectively combined according to an adaptive Lamarckian learning mechanism. In addition, an adaptive dominant replacement scheme, which can probabilistically accept inferior chromosomes, is also introduced into the proposed algorithm to enhance the diversity level of the population. Experimental results on a series of dynamic problems generated from several stationary benchmark problems show that the proposed algorithm is a good optimizer for DOPs.This work was supported in part by the National Nature Science Foundation of China (NSFC) under Grant 70431003 and Grant 70671020, by the National Innovation Research Community Science Foundation of China under Grant 60521003, by the National Support Plan of China under Grant 2006BAH02A09, by the Engineering and Physical Sciences Research Council (EPSRC) of U.K. under Grant EP/E060722/1, and by the Hong Kong Polytechnic University Research Grants under Grant G-YH60

Evolutionary algorithms in dynamic environments

The file attached to this record is the author's final peer reviewed version.Evolutionary algorithms (EAs) are widely and often used for solving stationary optimization problems where the fitness landscape or objective function does not change during the course of computation. However, the environments of real world optimization problems may fluctuate or change sharply. If the optimization problem is dynamic, the goal is no longer to find the extrema, but to track their progression through the search space as closely as possible. All kinds of approaches that have been proposed to make EAs suitable for the dynamic environments are surveyed, such as increasing diversity, maintaining diversity, memory based approaches, multi-population approaches and so on

Untying Gordian knots: The evolution and biogeography of the large European apomictic polyploid Ranunculus auricomus plant complex

Polyploidie, das Vorhandensein von zwei oder mehr vollständigen Chromosomensätzen, tritt wiederholt über den gesamten Baum des Lebens auf. Bei Pflanzen ist die wirtschaftliche, aber vor allem auch die evolutionäre Bedeutung überwältigend. Polyploidisierungen, wahrscheinlich verbunden mit Schlüsselinnovationen (z.B. die Entwicklung der Gefäßelemente oder des Fruchtblattes), traten in der Evolution der Blütenpflanzen häufig auf. Blütenpflanzen sind die artenreichste Gruppe im Pflanzenreich mit ca. 370,000 Arten und umfassen 30–70% Neopolyploide. Es wird angenommen, dass Polyploidie und Hybridisierung (Allopolyploidie) besonders zur Entstehung von Biotypen mit neuartiger genomischer Zusammensetzung beitragen und damit Schlüsselfaktoren für nachfolgende Artbildungen und Makroevolution sind. Bei Pflanzen sind beide Prozesse häufig mit Apomixis, der Reproduktion über asexuell gebildete Samen, verbunden. Das rätselhafte Phänomen der von Polyploidie und Apomixis begleiteten Artbildung ist jedoch trotz enormer Fortschritte auf dem Gebiet der Genomik noch immer kaum verstanden. Die Frage „Was ist eine Art?“ hat für Evolutionsbiologen höchste Priorität: Arten sind die Grundlage der Biodiversitätsforschung, und die evolutionäre und ökologische Forschung stützt sich auf gut definierte Einheiten. Evolutionär junge Artkomplexe bieten eine einzigartige Möglichkeit die Artbildung bei Pflanzen und deren begleitende Prozesse zu erforschen und zu verstehen. Sie umfassen meist wenige sexuelle Stammarten und zahlreiche polyploide, teilweise apomiktische, hybridogene Derivate. Das Fehlen von Rekombination und Kreuzbestäubung in apomiktischen Linien kann zu einer Vielzahl klonaler Hybridlinien mit fixierten morphologischen und ökologischen Merkmalen führen (Agamospezies). Selbst das Erkennen und Abgrenzen der sexuellen Stammarten ist aufgrund geringer genetischer Divergenz, eventuellen hybridogenen Ursprüngen, stetigem Genfluss und/oder unvollständiger genetischer Auftrennung der Abstammungslinien (ILS) methodisch herausfordernd. Integrative Ansätze, die sowohl genomische als auch morphometrische Daten verwenden, um die jungen Stammarten aufzutrennen, fehlen bisher. Die Biogeographie und Evolution der Artkomplexe ist weitaus komplexer. Apomikten besetzen im Vergleich zu ihren sexuellen Verwandten häufig größere Areale oder sind in nördlicheren Regionen verbreitet, ein Phänomen, das als Geographische Parthenogenese (GP) bezeichnet wird. GP-Muster haben meist einen pleistozänen Kontext. Klimatische Schwankungen in den gemäßigten und borealen Zonen boten häufig Möglichkeiten zur interspezifischen Hybridisierung, was wahrscheinlich auch zur Entstehung von Apomixis auf der Nordhalbkugel geführt hat. Faktoren, die diese Muster erzeugen, werden immer noch kontrovers diskutiert. GP-Muster wurden bisher oft den Vorteilen apomiktischer Populationen aufgrund von (Allo)polyploidie und uniparentaler Fortpflanzung zugeschrieben: Fixierte, hohe Heterozygotie führt zu einer erhöhten Stresstoleranz, und Selbstfertilität bedingt eine bessere Kolonisierungsfähigkeit. Einerseits sind die komplexen Wechselwirkungen von genomweiter Heterozygotie, Ploidie, Reproduktionssmodi (sexuell versus asexuell) und klimatischer Umweltfaktoren auf GP-Muster nicht ausreichend untersucht worden, andererseits wurden potentielle Nachteile sexueller Stammarten aufgrund ihres Fortpflanzungssystems auf Fitness und genetische Vielfalt bisher kaum betrachtet. Schließlich sind neben der Biogeographie die retikulate Evolution und die genomische Zusammensetzung und Evolution junger, großer polyploider Pflanzenartenkomplexe noch nicht detailliert entschlüsselt worden. Neben Herausforderungen, die auf eine hohe Anzahl an Polyploidisierungs- und Hybridisierungsereignissen zurückzuführen sind, werden bioinformatische Analysen oft durch fehlende Informationen zu sexuellen Stammarten, Ploidiegraden und Reproduktionsmodi erschwert. Der europäische, polyploid-apomiktische Ranunculus auricomus (Gold-Hahnenfuß) Pflanzenkomplex ist gut geeignet, um alle aufgeworfenen Fragestellungen zu untersuchen. Der Komplex entstand wahrscheinlich durch unzählige Hybridisierungen weniger sexueller Stammarten. Bisher wurden mehr als 800 morphologisch sehr diverse Agamospezies (Derivate) beschriebenen. Die sexuellen Stammarten werden weniger als 1.0 Millionen Jahren alt geschätzt, und die Agamospezies sind wahrscheinlich noch viel jünger. In meiner Dissertation habe ich unter Verwendung des R. auricomus Komplexes als Modellsystem die bisher wenig verstandenen phylogenetischen, genomischen und biogeographischen Beziehungen junger, polyploider Pflanzengruppen untersucht. Ich habe einen umfassenden theoretischen und bioinformatischen Workflow entwicklelt, beginnend mit der Untersuchung der Evolution der sexuellen Stammarten, über die Entschlüsselung der Reproduktionsmodi und Biogeographie polyploid-apomiktischer Derivate bis hin zur Aufdeckung der retikulaten Ursprünge und Genomzusammensetzung und -evolution des Polyploidkomplexes. Diese Arbeit umfasst 251 Populationen und 87 R. auricomus Taxa europaweit. Die Analysen basieren auf 97,312 genomischen Loci (RADseq), 663 Kerngenen (target enrichment) und 71 Plastidenregionen, und 1,474 Blattploidie-, 4,669 Reproduktions- Samen-, 284 Kreuzungs- (Samenansatz), und 1,593 Morphometrie-Messungen. Phylogenomische Daten basierend auf RADseq, Kerngenen und geometrischer Morphometrie unterstützten die Zusammenlegung der zwölf sexuellen Morphospezies in fünf neu klassifizierte Stammarten. Diese Arten stellen klar unterscheidbare genetische Hauptlinien oder Cluster dar, die sowohl geographisch gut isoliert als auch morphologisch klar differenziert sind: R. cassubicifolius s.l., R. envalirensis s.l., R. flabellifolius, R. marsicus und R. notabilis s.l. Enorme retikulate Beziehungen innerhalb der Kladen, die nicht-vorhandene geographische Isolation und das Fehlen markanter morphologischer Merkmale haben zu diesem taxonomischen Konzept geführt. Allopatrische Artbildungsereignisse fanden interessanterweise vor ca. 0.83–0.58 Millionen Jahren während enormer klimatischer Schwankungen statt und wurden wahrscheinlich durch Vikarianzprozesse aus einer weit verbreiteten europäischen Stammart ausgelöst. Darüber hinaus wurde die neue Umschreibung der sexuellen Stammarten durch Populationskreuzungsexperimente unterstützt. Kreuzungen zeigten neben Inzuchtdepression, Auszuchtvorteilen und plötzlicher Selbstkompatibilität auch völlig fehlende Reproduktionsbarrieren zwischen einigen Morphospezies. Darüber hinaus wurden durchflusszytometrische Ploidy- und Reproduktions-, genomweite RADseq- und klimatische Umweltdaten in einer genetisch-informierten Pfadanalyse basierend auf Generalisierten Linearen Gemischten Modellen (GLMMs) kombiniert. Die Analyse hat ein komplexes europäisches GP-Szenario aufgedeckt, in der Diploide im Vergleich zu Polyploiden eine signifikant höhere Sexualität (Prozent sexueller Samen), mehr Blütenblätter (petaloide Nektarblätter) und bis zu dreimal weniger genomweite Heterozygotie zeigten. Die Sexualität war überaschenderweise positiv mit Sonneneinstrahlung und Isothermalität verbunden, und die Heterozygotie zeigte einen positiven Zusammenhang mit der Temperatursaisonalität. Die Ergebnisse stimmen mit der südlichen Verbreitung diploid-sexueller Populationen überein und deuten auf eine höhere Resistenz polyploid-apomiktischer Populationen gegenüber extremeren klimatischen Bedingungen hin. Ein neu entwickelter, multidisziplinärer Workflow, der alle bisherigen Daten einbezieht, deckte zum ersten Mal den weitestgehend allopolyploiden Ursprung und die Genomzusammensetzung und -evolution des R. auricomus Komplexes auf. Die Taxa waren in nur drei bis fünf unterstützten, nord-süd verbreiteten Kladen oder Clustern organisiert, die jeweils meistens diploid-sexuelle Stammarten enthielten. Allopolyploidisierungsereignisse bezogen jeweils zwei bis drei verschiedene, diploid-sexuelle Subgenome ein. Es wurde nur ein autotetraploides Ereignis nachgewiesen. Allotetraploide Genome sind gekennzeichnet durch Subgenomdominanz und einer enormen Evolution nach ihrer Entstehung (z.B. Mendelsche Segregation der Hybridgenerationen, Rückkreuzungen zu Elternarten und Genfluss aufgrund fakultativer Sexualität der Apomikten). Die über 800 Taxa des europäischen R. auricomus-Komplexes sind vermutlich aus vier diploiden Stammarten und eine bisher unbekannte, aktuell wahrscheinlich ausgestorbene Stammart, entstanden. Analysen zeigten auch, dass die Mehrzahl der beschriebenen polyploiden Agamospezies nicht monophyletisch ist und ähnliche Morphotypen wahrscheinlich mehrfach entstanden sind. Eine umfassende taxonomische Überarbeitung des gesamten Komplexes ist daher angebracht. In der Allgemeinen Diskussion kombiniere ich die Ergebnisse meiner Dissertation mit bereits existierenden Pflanzenstudien zur diploid-sexuellen und polyploid-apomiktischen Phylogenetik, Biogeographie und Genomzusammensetzung und -evolution junger Artkomplexe. Ich gebe zudem taxonomische Schlussfolgerungen und erkläre wie Artkomplexe mikro- und makroevolutionäre Prozesse miteinander verbinden. Abschließend gebe ich ein Fazit über die Ergebnisse meiner Dissertation und einen Ausblick für das laufende Forschungsprojekt und der Forschungsdisziplin der polyploiden Phylogenetik.Polyploidy, the presence of two or more full genomic complements, repeatedly occurs across the tree of life. In plants, not only the economic but particularly the evolutionary importance is overwhelming. Polyploidization events, probably connected to key innovations (e.g., vessel elements or the carpel), occurred frequently in the evolutionary history of flowering plants, which are the most species-rich group in the plant kingdom (ca. 370,000 species) and contain 30–70% neopolyploids. Polyploidy and hybridization (i.e., allopolyploidy) are particularly considered to create biotypes with novel genomic compositions and to be key factors for subsequent speciation and macroevolution. In plants, both processes are frequently connected to apomixis, i.e., the reproduction via asexually-formed seeds. However, the enigmatic phenomenon of plant speciation accompanied by polyploidy and apomixis is still poorly understood despite tremendous progress in the field of genomics. The question of “What is a species?” is of highest priority for evolutionary biologists: Species are the fundamental units for biodiversity, and further evolutionary and ecological research relies on well-defined entities. Evolutionarily young plant species complexes offer a unique opportunity to study plant speciation and accompanying processes. They usually comprise a few sexual progenitor species, and numerous polyploid, partly apomictic, hybrid derivatives. In apomictic lineages, the lack of recombination and cross-fertilization can result in numerous clonal lineages with fixed morphological and ecological traits (agamospecies). Nevertheless, even recognizing and delimiting the sexual progenitors of species complexes is methodically challenging due to low genetic divergence, possible hybrid origins, ongoing gene flow, and/or incomplete lineage sorting (ILS). Integrative approaches using both genomic and morphometric data for disentangling the young progenitors are still lacking so far. The biogeography and evolution of those plant complexes is even more challenging. Apomicts frequently occupy larger areas or more northern regions compared to their sexual relatives, a phenomenon called geographical parthenogenesis (GP). GP patterns usually have a Pleistocene context because climatic range shifts in temperate to boreal zones offered frequent opportunities for interspecific hybridization, probably giving rise to apomixis in the Northern Hemisphere. Factors shaping GP patterns are still controversially discussed. GP has been widely attributed to advantages of apomicts caused by polyploidy and uniparental reproduction, i.e., fixed levels of high heterozygosity leading to increased stress tolerance, and self-fertility leading to better colonizing capabilities. On the one hand, complex interactions of genome-wide heterozygosity, ploidy, reproduction mode (sexual versus asexual), and climatic environmental factors shaping GP have not been studied enough. On the other hand, potential disadvantages of sexual progenitors due to their breeding system on fitness and genetic diversity have received even less attention. Finally, alongside biogeography, the reticulate relationships and genome composition and evolution of young, large polyploid plant species complexes have not yet been deciphered comprehensively. Besides challenges attributed to numerous numbers of polyploidization and hybridization events, bioinformatic analyses are also often hampered by missing information on progenitors, ploidy levels, and reproduction modes. The European apomictic polyploid Ranunculus auricomus (goldilock buttercup) plant complex is well-suited to study all the aforementioned issues. The majority of goldilock buttercups probably arose from hybridization of a few sexual progenitors, leading to more than 800 described, morphologically highly diverse agamospecies. Sexuals are estimated to have speciated less than 1.0 million years ago, and agamospecies are probably much younger. In this thesis, using R. auricomus as a model system, I examined the recalcitrant and hitherto poorly understood phylogenetic, genomic, and biogeographical relationships of young polyploid apomictic plant complexes. I developed a comprehensive theoretical and bioinformatic workflow, starting with analyzing the evolution of the sexual progenitor species, continuing with unraveling reproduction modes and biogeography of apomictic polyploids, and ending up with revealing the reticulate origins and genome composition and evolution of the polyploid complex. Spanning up to 251 populations and 87 R. auricomus taxa Europe-wide, this work gathered data of 97,312 genomic loci (RADseq), 663 nuclear genes (target enrichment), and 71 plastid regions, and 1,474 leaf ploidy, 4,669 reproductive seed, 284 reproductive crossing (seed sets), as well as 1,593 geometric morphometric measurements. First of all, phylogenomics based on RADseq, nuclear gene, and geometric morphometric data supported the lumping of the twelve described sexual morphospecies into five newly circumscribed progenitor species. These species represent clearly distinguishable genetic main lineages or clusters, which are both well geographically isolated and morphologically differentiated: R. cassubicifolius s.l., R. envalirensis s.l., R. flabellifolius, R. marsicus, and R. notabilis s.l. Mainly within-clade reticulate relationships, missing geographical isolation, and a lack of distinctive morphological characters led to this taxonomic treatment. Interestingly, allopatric speciation events took place ca. 0.83–0.58 million years ago during a period of severe climatic oscillations, and were probably triggered by vicariance processes of a widespread European forest-understory ancestor. Sexual species re-circumscriptions were additionally supported by population crossing experiments. Besides inbreeding depression, outbreeding benefits, and sudden self-compatibility, crossings also revealed a lack of reproductive barriers among some of the formerly described morphospecies. Moreover, flow cytometric ploidy and reproductive, RADseq, and environmental data were combined into a genetically informed path analysis based on Generalized Linear Mixed Models (GLMMs). The analysis unveiled a complex European GP scenario, whereby diploids compared to polyploids showed significantly higher sexuality (percent of sexual seeds), more petals (petaloid nectary leaves), and up to three times less genome-wide heterozygosity. Surprisingly, sexuality was positively associated with solar radiation and isothermality, and heterozygosity was positively related to temperature seasonality. Results fit the southern distribution of diploid sexuals and suggest a higher resistance of polyploid apomicts to more extreme climatic conditions. Finally, a self-developed, multidisciplinary workflow incorporating all previously gathered data demonstrated, for the first time, the predominantly allopolyploid origin, genome composition, and post-origin genome evolution of the R. auricomus complex. Taxa were organized in only three to five supported, north-south distributed clades or cluster, each usually containing diploid sexual progenitor species. Allopolyploidizations involved two to three different diploid sexual subgenomes per event. Only one autotetraploid event was detected. Allotetraploids were characterized by subgenome dominance and enormous post-origin evolution, i.e., Mendelian segregation of hybrid generations, back-crossing to parents, and/or gene flow due to facultative sexuality of apomicts. Four diploid sexual progenitors and a previously unknown, nowadays extinct progenitor, probably gave rise to the more than 800 taxa of the European R. auricomus complex. Analyses also showed that the majority of analyzed polyploid agamospecies are non-monophyletic and similar morphotypes probably originated multiple times. The lack of monophyly suggests a comprehensive taxonomic revision of the entire complex. In the General Discussion, I combine my thesis results with existing plant studies on diploid sexual and polyploid apomictic phylogenetics, biogeography, and composition and genome evolution of young species complexes. I explain the taxonomic conclusions and how species complexes link micro- and macroevolutionary processes. Finally, I give conclusions of my thesis and an outlook of the project and the field of polyploid phylogenetics.2021-10-2

Characterization of a large sex determination region in Salix purpurea L. (Salicaceae).

Dioecy has evolved numerous times in plants, but heteromorphic sex chromosomes are apparently rare. Sex determination has been studied in multiple Salix and Populus (Salicaceae) species, and P. trichocarpa has an XY sex determination system on chromosome 19, while S. suchowensis and S. viminalis have a ZW system on chromosome 15. Here we use whole genome sequencing coupled with quantitative trait locus mapping and a genome-wide association study to characterize the genomic composition of the non-recombining portion of the sex determination region. We demonstrate that Salix purpurea also has a ZW system on chromosome 15. The sex determination region has reduced recombination, high structural polymorphism, an abundance of transposable elements, and contains genes that are involved in sex expression in other plants. We also show that chromosome 19 contains sex-associated markers in this S. purpurea assembly, along with other autosomes. This raises the intriguing possibility of a translocation of the sex determination region within the Salicaceae lineage, suggesting a common evolutionary origin of the Populus and Salix sex determination loci

Somatic mutations and clonal dynamics in healthy and cirrhotic human liver.

The most common causes of chronic liver disease are excess alcohol intake, viral hepatitis and non-alcoholic fatty liver disease, with the clinical spectrum ranging in severity from hepatic inflammation to cirrhosis, liver failure or hepatocellular carcinoma (HCC). The genome of HCC exhibits diverse mutational signatures, resulting in recurrent mutations across more than 30 cancer genes1-7. Stem cells from normal livers have a low mutational burden and limited diversity of signatures8, which suggests that the complexity of HCC arises during the progression to chronic liver disease and subsequent malignant transformation. Here, by sequencing whole genomes of 482 microdissections of 100-500 hepatocytes from 5 normal and 9 cirrhotic livers, we show that cirrhotic liver has a higher mutational burden than normal liver. Although rare in normal hepatocytes, structural variants, including chromothripsis, were prominent in cirrhosis. Driver mutations, such as point mutations and structural variants, affected 1-5% of clones. Clonal expansions of millimetres in diameter occurred in cirrhosis, with clones sequestered by the bands of fibrosis that surround regenerative nodules. Some mutational signatures were universal and equally active in both non-malignant hepatocytes and HCCs; some were substantially more active in HCCs than chronic liver disease; and others-arising from exogenous exposures-were present in a subset of patients. The activity of exogenous signatures between adjacent cirrhotic nodules varied by up to tenfold within each patient, as a result of clone-specific and microenvironmental forces. Synchronous HCCs exhibited the same mutational signatures as background cirrhotic liver, but with higher burden. Somatic mutations chronicle the exposures, toxicity, regeneration and clonal structure of liver tissue as it progresses from health to disease.This work was supported by a Wellcome Trust and Cancer Research UK (CRUK) Grand Challenge Award (C98/A24032). P.J.C. is a Wellcome Trust Senior Clinical Fellow (WT088340MA); S.F.B. was supported by the Swiss National Science Foundation (P2SKP3-171753 and P400PB-180790); M.A.S. is supported by a Rubicon fellowship from NWO (019.153LW.038); the Cambridge Human Research Tissue Bank is supported by the NIHR Cambridge Biomedical Research Centre; and M.H. is supported by a CRUK Clinician Scientist Fellowship (C52489/A19924)

Genome-wide analysis of the omega-3 fatty acid desaturase gene family in Gossypium

Background The majority of commercial cotton varieties planted worldwide are derived from Gossypium hirsutum, which is a naturally occurring allotetraploid produced by interspecific hybridization of A- and D-genome diploid progenitor species. While most cotton species are adapted to warm, semi-arid tropical and subtropical regions, and thus perform well in these geographical areas, cotton seedlings are sensitive to cold temperature, which can significantly reduce crop yields. One of the common biochemical responses of plants to cold temperatures is an increase in omega-3 fatty acids, which protects cellular function by maintaining membrane integrity. The purpose of our study was to identify and characterize the omega-3 fatty acid desaturase (FAD) gene family in G. hirsutum, with an emphasis on identifying omega-3 FADs involved in cold temperature adaptation. Results Eleven omega-3 FAD genes were identified in G. hirsutum, and characterization of the gene family in extant A and D diploid species (G. herbaceum and G. raimondii, respectively) allowed for unambiguous genome assignment of all homoeologs in tetraploid G. hirsutum. The omega-3 FAD family of cotton includes five distinct genes, two of which encode endoplasmic reticulum-type enzymes (FAD3-1 and FAD3-2) and three that encode chloroplast-type enzymes (FAD7/8-1, FAD7/8-2, and FAD7/8-3). The FAD3-2 gene was duplicated in the A genome progenitor species after the evolutionary split from the D progenitor, but before the interspecific hybridization event that gave rise to modern tetraploid cotton. RNA-seq analysis revealed conserved, gene-specific expression patterns in various organs and cell types and semi-quantitative RT-PCR further revealed that FAD7/8-1 was specifically induced during cold temperature treatment of G. hirsutum seedlings. Conclusions The omega-3 FAD gene family in cotton was characterized at the genome-wide level in three species, showing relatively ancient establishment of the gene family prior to the split of A and D diploid progenitor species. The FAD genes are differentially expressed in various organs and cell types, including fiber, and expression of the FAD7/8-1 gene was induced by cold temperature. Collectively, these data define the genetic and functional genomic properties of this important gene family in cotton and provide a foundation for future efforts to improve cotton abiotic stress tolerance through molecular breeding approaches