Isolating an active and inactive CACTA transposon from lettuce color mutants and characterizing their family

Gurdon, Csanad; Kozik, Alexander; Tao, Rong; Poulev, Alexander; Armas, Isabel; Michelmore, Richard W.; Raskin, Ilya

doi:10.1093/plphys/kiab143

Cited by 6 publications

(15 citation statements)

References 76 publications

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“…The TEs account for 74.2% of the lettuce genome (Reyes- Chin-Wo et al, 2017). Thus, transposons may play an important role in the evolution of lettuce (Gurdon et al, 2021;Yu et al, 2020). In this study, we found that a CACTA transposon was inserted into the 3 0 -UTR of LsGLK and that this insertion led to the development of pale-green leaves.…”

Section: Alternative Splicing Triggered By Transposons Contributes To Phenotypic Variationmentioning

confidence: 59%

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Alternative splicing triggered by the insertion of a CACTA transposon attenuates LsGLK and leads to the development of pale‐green leaves in lettuce

et al. 2021

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Lettuce (Lactuca sativa) is one of the most important vegetable crops in the world. As a leafy vegetable, the polymorphism of lettuce leaves from dark to pale green is an important trait. However, the genetic and molecular mechanisms underlying such variations remain poorly understood. In this study, one major locus controlling the polymorphism of dark-and pale-green leaves in lettuce was identified using genome-wide association studies (GWAS). This locus was then fine mapped to an interval of 5375 bp on chromosome 4 using a segregating population containing 2480 progeny. Only one gene, homologous to the GLK genes in Arabidopsis and other plants, is present in the candidate region. A complementation test confirmed that the candidate gene, LsGLK, contributes to the variation of dark-and pale-green leaves. Sequence analysis showed that a CACTA transposon of 7434 bp was inserted 10 bp downstream of the stop codon of LsGLK, followed by a duplication of a 1826-bp fragment covering exons 3-6 of the LsGLK gene. The transposon insertion did not change the expression level of the LsGLK gene. However, because of alternative splicing, only 6% of the transcripts produced from the transposon insertion were wild-type transcripts, which led to the production of pale-green leaves. An evolutionary analysis revealed that the insertion of the CACTA transposon occurred in cultivated lettuce and might have been selected in particular cultivars to satisfy the diverse demands of consumers. In this study, we demonstrated that a transposon insertion near a gene may affect its splicing and consequently generate phenotypic variations.

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Section: Alternative Splicing Triggered By Transposons Contributes To Phenotypic Variationmentioning

confidence: 59%

“…The red color of lettuce has been well characterized. At least four polymorphic genes associated with red leaves were identified (Gurdon et al, 2021;Su et al, 2020;Zhang et al, 2017). The variations in the green color of lettuce leaves were preliminarily studied.…”

Section: Introductionmentioning

confidence: 99%

Alternative splicing triggered by the insertion of a CACTA transposon attenuates LsGLK and leads to the development of pale‐green leaves in lettuce

et al. 2021

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“…One of the QTLs for the content of chlorophyll (qLG4.1) was previously detected in multiple mapping populations (Kwon et al, 2013;Simko et al, 2016;Mamo et al, 2019;Parra et al, 2021, Simko et al, unpublished results), while the other three QTLs appeared to be located at the genomic regions not previously associated with the content of chlorophyll. Out of 12 QTLs for the content of anthocyanins, 7 (qRLC2.1, RLL3, RLL2, qRLC5.2, qRLC7.2, RLL4, and ANS) were found at or near QTLs and genes for red leaf color or anthocyanin content detected in previous studies (Kwon et al, 2013;Mamo et al, 2019;Gurdon et al, 2021;Simko et al, 2022b, Simko et al, unpublished results, Zhang et al, 2017Su et al, 2020;Wei et al, 2021;Wada et al, 2022), while the remaining five QTLs were new.…”

Section: Phenotypic Relationship Of Pigments Plant Development and Th...mentioning

confidence: 73%

“…In recent years, INSV has emerged as a primary threat to the lettuce industry in the Western United States (Hasegawa and Del Kwon et al, 2013;Simko et al, 2016;Mamo et al, 2019;Parra et al, 2021, Simko et al, unpublished Kwon et al, 2013;Mamo et al, 2019;Gurdon et al, 2021;Simko et al, 2022b, Simko et al, unpublished results, Zhang et al, 2017Su et al, 2020;Wei et al, 2021;Wada et al, 2022) a If a QTL detected in the current study is located in the same or an adjacent bin as a QTL/gene detected in previous studies, it gets the same name as the previously detected QTL/gene. Pozo-Valdivia, 2022;Hasegawa et al, 2022).…”

Section: Discussionmentioning

confidence: 99%

Genetic and physiological determinants of lettuce partial resistance to Impatiens necrotic spot virus

Šimko¹,

Hasegawa²,

Peng³

et al. 2023

Front. Plant Sci.

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IntroductionImpatiens necrotic spot virus (INSV) is a major pathogen currently threatening lettuce (Lactuca sativa L.) production in the coastal areas of California. The virus is transmitted by the western flower thrips (Frankliniella occidentalis Pergande).MethodsWe have tested a diversity panel of almost 500 lettuce accessions for disease incidence (DI) in 12 field experiments performed over 7 years. This set of accessions was also assessed for thrips feeding damage (TFD), the rate of plant development (PD), and the content of chlorophyll (SPAD) and anthocyanins (ACI) to determine their effect on resistance to INSV. In addition, recombinant inbred lines from two biparental mapping populations were also evaluated for DI in field experiments.ResultsThe mean DI in 14 field experiments ranged from 2.1% to 70.4%. A highly significant difference in DI was observed among the tested accessions, with the overall lowest DI detected in the red color cultivars, Outredgeous Selection, Red Splash Cos, Infantry, Sweet Valentine, Annapolis, and Velvet. Multiple linear regression models revealed a small but significant effect (p < 0.005) of the four analyzed determinants on DI. Accessions with lower DI values had slower plant development (PD, r = 0.352), higher ACI content (r = −0.284), lower TFD (r = 0.198), and lower SPAD content (r = 0.125). A genome-wide association study revealed 13 QTLs for DI located on eight out of the nine lettuce chromosomes (the exception was chr. 8). The most frequently detected QTL (qINSV2.1) was located on chr. 2. Several of the QTLs for DI were in the same genomic areas as QTLs for PD, ACI, and SPAD. Additional three QTLs for DI on chr. 5 and 8 were identified using linkage mapping performed on two biparental mapping populations.ConclusionsThe work highlights the genetic basis of partial resistance to INSV and reveals the relationship between resistance, the host physiology, and the thrips vector. Results of this study are an important steppingstone toward developing cultivars with increased resistance against INSV.

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“…CACTA transposons are one of the most abundant superfamilies of DNA transposons (Tian, 2006;Wicker et al, 2007;Sergeeva et al, 2010;Lisch, 2013;Belyayev et al, 2022). It has been reported that CACTA transposons constitute c. 2-15% of plant genomes (Paterson et al, 2009;Vogel et al, 2010;Gurdon et al, 2021;Z. Y. Wang et al, 2022).…”

Section: The Multifaceted Effects Of Cacta Transposons In Gene Functionsmentioning

confidence: 99%

A WOX homolog disrupted by a transposon led to the loss of spines and contributed to the domestication of lettuce

Sun,

Yuan,

Pan

et al. 2024

New Phytologist

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Summary The loss of spines is one of the most important domestication traits for lettuce (Lactuca sativa). However, the genetics and regulation of spine development in lettuce remain unclear. We examined the genetics of spines in lettuce using a segregating population derived from a cross between cultivated and wild lettuce (Lactuca serriola). A gene encoding WUSCHEL‐related homeobox transcription factor, named as WOX‐SPINE1 (WS1), was identified as the candidate gene controlling the spine development in lettuce, and its function on spines was verified. A CACTA transposon was found to be inserted into the first exon of the ws1 allele, knocking out its function and leading to the lack of spines in cultivated lettuce. All lettuce cultivars investigated have the nonfunctional ws1 gene, and a selection sweep was found at the WS1 locus, suggesting its important role in lettuce domestication. The expression levels of WS1 were associated with the density of spines among different accessions of wild lettuce. At least two independent loss‐of‐function mutations in the ws1 gene caused the loss of spines in wild lettuce. These findings provide new insights into the development of spines and facilitate the exploitation of wild genetic resources in future lettuce breeding programs.

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Isolating an active and inactive CACTA transposon from lettuce color mutants and characterizing their family

Cited by 6 publications

References 76 publications

Alternative splicing triggered by the insertion of a CACTA transposon attenuates LsGLK and leads to the development of pale‐green leaves in lettuce

Alternative splicing triggered by the insertion of a CACTA transposon attenuates LsGLK and leads to the development of pale‐green leaves in lettuce

Genetic and physiological determinants of lettuce partial resistance to Impatiens necrotic spot virus

A WOX homolog disrupted by a transposon led to the loss of spines and contributed to the domestication of lettuce

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