A molecular perspective on the taxonomy and journey of Citrus domestication

Kalita, Barsha; Roy, Abhijeet Deb; Annamalai, A.; Lakshmi, P.T.V.

doi:10.1016/j.ppees.2021.125644

Cited by 10 publications

(6 citation statements)

References 116 publications

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“…If an individual genotype suggests mixing, they are allocated to a population or many populations. The majority of genetic marker systems may be used in this technique to estimate population structure, given that the markers are not strongly connected 7 , 37 , 39 , 68 . It makes no assumptions about the specific mutation process 37 .…”

Section: Discussionmentioning

confidence: 99%

“…It is a popular fruit crop that is recognised for its energising scent, high vitamin C content, and health-promoting properties 6 . Therefore, citrus fruits are in high demand all around the world 7 . Citrus taxonomy is complicated by the peculiar manner of reproduction, a high frequency of bud mutations, apomictic, and the species extensive cross-compatibility 7 – 10 .…”

Section: Introductionmentioning

confidence: 99%

“…Therefore, citrus fruits are in high demand all around the world 7 . Citrus taxonomy is complicated by the peculiar manner of reproduction, a high frequency of bud mutations, apomictic, and the species extensive cross-compatibility 7 – 10 . However, on the other hand conventional citrus breeding takes at least 3–8 years to complete due to the lengthy juvenile stage 2 .…”

Section: Introductionmentioning

confidence: 99%

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Comprehensive genome-wide identification and transferability of chromosome-specific highly variable microsatellite markers from citrus species

Singh

Sharma

et al. 2023

Sci Rep

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Citrus species among the most important and widely consumed fruit in the world due to Vitamin C, essential oil glands, and flavonoids. Highly variable simple sequence repeats (SSR) markers are one of the most informative and versatile molecular markers used in perennial tree genetic research. SSR survey of Citrus sinensis and Citrus maxima were identified perfect SSRs spanning nine chromosomes. Furthermore, we categorized all SSR motifs into three major classes based on their tract lengths. We designed and validated a class I SSRs in the C. sinensis and C. maxima genome through electronic polymerase chain reaction (ePCR) and found 83.89% in C. sinensis and 78.52% in C. maxima SSRs producing a single amplicon. Then, we selected extremely variable SSRs (> 40 nt) from the ePCR-verified class I SSRs and in silico validated across seven draft genomes of citrus, which provided us a subset of 84.74% in C. sinensis and 77.53% in C. maxima highly polymorphic SSRs. Out of these, 129 primers were validated on 24 citrus genotypes through wet-lab experiment. We found 127 (98.45%) polymorphic HvSSRs on 24 genotypes. The utility of the developed HvSSRs was demonstrated by analysing genetic diversity of 181 citrus genotypes using 17 HvSSRs spanning nine citrus chromosomes and were divided into 11 main groups through 17 HvSSRs. These chromosome-specific SSRs will serve as a powerful genomic tool used for future QTL mapping, molecular breeding, investigation of population genetic diversity, comparative mapping, and evolutionary studies among citrus and other relative genera/species.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Comprehensive genome-wide identification and transferability of chromosome-specific highly variable microsatellite markers from citrus species

Singh

Sharma

et al. 2023

Sci Rep

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“…Our current knowledge on citrus domestication is still very unprecise (Deng et al, 2020;Kalita et al, 2021;Rao et al, 2021). During the last years, most attention has been paid to the identification of genes or gene families impacting palatability traits, fruit characteristics and reproductive behavior.…”

Section: Introductionmentioning

confidence: 99%

Transcriptome analysis of the pulp of citrus fruitlets suggests that domestication enhanced growth processes and reduced chemical defenses increasing palatability

et al. 2022

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To identify key traits brought about by citrus domestication, we have analyzed the transcriptomes of the pulp of developing fruitlets of inedible wild Ichang papeda (Citrus ichangensis), acidic Sun Chu Sha Kat mandarin (C. reticulata) and three palatable segregants of a cross between commercial Clementine (C. x clementina) and W. Murcott (C. x reticulata) mandarins, two pummelo/mandarin admixtures of worldwide distribution. RNA-seq comparison between the wild citrus and the ancestral sour mandarin identified 7267 differentially expressed genes, out of which 2342 were mapped to 117 KEGG pathways. From the remaining genes, a set of 2832 genes was functionally annotated and grouped into 45 user-defined categories. The data suggest that domestication promoted fundamental growth processes to the detriment of the production of chemical defenses, namely, alkaloids, terpenoids, phenylpropanoids, flavonoids, glucosinolates and cyanogenic glucosides. In the papeda, the generation of energy to support a more active secondary metabolism appears to be dependent upon upregulation of glycolysis, fatty acid degradation, Calvin cycle, oxidative phosphorylation, and ATP-citrate lyase and GABA pathways. In the acidic mandarin, downregulation of cytosolic citrate degradation was concomitant with vacuolar citrate accumulation. These changes affected nitrogen and carbon allocation in both species leading to major differences in organoleptic properties since the reduction of unpleasant secondary metabolites increases palatability while acidity reduces acceptability. The comparison between the segregants and the acidic mandarin identified 357 transcripts characterized by the occurrence in the three segregants of additional downregulation of secondary metabolites and basic structural cell wall components. The segregants also showed upregulation of genes involved in the synthesis of methyl anthranilate and furaneol, key substances of pleasant fruity aroma and flavor, and of sugar transporters relevant for sugar accumulation. Transcriptome and qPCR analysis in developing and ripe fruit of a set of genes previously associated with citric acid accumulation, demonstrated that lower acidity is linked to downregulation of these regulatory genes in the segregants. The results suggest that the transition of inedible papeda to sour mandarin implicated drastic gene expression reprograming of pivotal pathways of the primary and secondary metabolism, while palatable mandarins evolved through progressive refining of palatability properties, especially acidity.

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“…Our current knowledge on citrus domestication is still very unprecise (Deng et al, 2020;Rao et al, 2021;Kalita et al, 2021). During the last years, most attention has been paid…”

Section: Introductionmentioning

confidence: 99%

Mutation Rate and Gene Expression in Genetic Admixtures of Domesticated Citrus

Román¹

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Citrus domestication is a largely unknown process. Research carried out to date indicates that current commercial citrus varieties are, in general, the product of ancestral intraspecific and interspecific introgressions. Intraspecific introgressions took place Es difícil delinear con nombres propios un plural tan amplio. Difícil y arriesgado. Por eso, seré breve.En primer lugar, he de destacar el papel indispensable de mis compañeros del Centro de Genómica del IVIA. Todos ellos han posibilitado de algún modo este trabajo. No hace falta nombraros, sabéis quien sois.De manera especial, sin embargo, quiero reconocer como, desde el primer momento, la respuesta a todas mis dudas, inseguridades y falta de criterio la he encontrado en ti. Has sido el ejemplo que mi actitud necesitaba. Sin más, gracias, Carles.Del mismo modo, debo admitir que adentrarse en el mundo científico guiada por la competencia del apellido Talón ha sido un honor a todos los niveles. Cada palabra de este trabajo es garante de ese hecho. Gracias a ti también, Manolo. I, siga com siga, aquestes paraules no poden obviar altres certeses que, si bé resulten menys pragmàtiques, esdevenen igualment importants. Per això, he de confessar que ha sigut alliberador comprovar com l'amistat no entén de condicions. Amb un significat que-sortosament per a mi-desmereix el de cada errada que l'amenaça, avançar ha sigut l'única possibilitat.En aquest sentit, el triomf personal més valuós que he assolit ha estat trobar en els anys, els bacs i l'experiència viscuda durant aquesta etapa l'oportunitat de reafirmar-me en allò que sempre he sospitat. I, és que, al remat, la conclusió no pot ser diferent: la meua sort porta el vostre nom. Gràcies,

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A molecular perspective on the taxonomy and journey of Citrus domestication

Cited by 10 publications

References 116 publications

Comprehensive genome-wide identification and transferability of chromosome-specific highly variable microsatellite markers from citrus species

Comprehensive genome-wide identification and transferability of chromosome-specific highly variable microsatellite markers from citrus species

Transcriptome analysis of the pulp of citrus fruitlets suggests that domestication enhanced growth processes and reduced chemical defenses increasing palatability

Mutation Rate and Gene Expression in Genetic Admixtures of Domesticated Citrus

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