Genetic and gene expression analysis of flowering time regulation by light quality in lentil

Yuan, Huajun; Caron, Carolyn T.; Ramsay, Larissa; Fratini, Richard; Vega, M. Pérez de la; Vandenberg, Albert; Weller, James L.; Bett, Kirstin E.

doi:10.1093/aob/mcab083

Cited by 16 publications

(15 citation statements)

References 83 publications

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“…In a recent study parallel to this one, interspecific genetic analysis of flowering time differences between L. culinaris and its putative wild ancestor L. orientalis also revealed a QTL co-locating with qDTF6a , and identified FTa1 as the only differentially regulated candidate gene within the QTL interval ( Yuan et al , 2021 ). Interestingly, in this case, FTa1 expression was higher, and flowering was earlier, in the wild parent relative to the domesticated parent cv.…”

Section: Discussionmentioning

confidence: 81%

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Genetic analysis of early phenology in lentil identifies distinct loci controlling component traits

Rajandran

Ortega

Schoor

et al. 2022

Journal of Experimental Botany

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Modern-day domesticated lentil germplasm is generally considered to form three broad adaptation groups: Mediterranean, South Asian and northern temperate, which correspond to the major global production environments. Reproductive phenology plays a key role in lentil adaptation to this diverse ecogeographic variation. Here, we dissect the characteristic earliness of the pilosae ecotype, suited to the typically short cropping season of South Asian environments. We identified two loci, DTF6a and DTF6b, at which dominant alleles confer early flowering, and we show that DTF6a alone is sufficient to confer early flowering under extremely short photoperiods. Genomic synteny confirmed the presence of a conserved cluster of three florigen (FT) gene orthologs among potential candidate genes, and expression analysis in near-isogenic material showed that the early allele is associated with a strong derepression of the FTa1 gene in particular. Sequence analysis revealed a 7.4 kb deletion in the FTa1-FTa2 intergenic region in the pilosae parent, and a wide survey of over 350 accessions with diverse origin showed that the dtf6a allele is predominant in South Asian material. Collectively, these results contribute to understanding the molecular basis of global adaptation in lentil, and further emphasize the importance of this conserved genomic region for adaptation in temperate legumes generally.

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Section: Discussionmentioning

confidence: 81%

“…The closely related species pea has six FT genes ( Hecht et al , 2011 ; Ortega et al , 2019 ), and an analysis of the recently released lentil genome sequence has confirmed that the same is also true in lentil ( Yuan et al , 2021 ; Supplementary Fig. S5 ).…”

Section: Resultsmentioning

confidence: 89%

Genetic analysis of early phenology in lentil identifies distinct loci controlling component traits

Rajandran

Ortega

Schoor

et al. 2022

Journal of Experimental Botany

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“…The closely related species pea has six FT genes (Hecht et al 2011; Ortega et al 2019), and an analysis of recently released lentil genome sequence has confirmed that the same is also true in lentil (Yuan et al 2021, Supp Figure 5 ). The results in Figure 5B show that in leaf tissue of three-weeks old plants grown under SD conditions, both FTa1 and FTa2 genes were expressed at a significantly higher level in NILs carrying the dtf6a allele compared to equivalent plants with the DTF6a allele.…”

Section: Resultsmentioning

confidence: 88%

Genetic analysis of early phenology in lentil identifies distinct loci controlling component traits

Weller

Hecht

Martinez

et al. 2021

Preprint

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Reproductive phenology is well known to be a key feature of crop adaptation to diverse ecogeographic variation and management practices. Lentil is one of the founder pulse crops of middle-eastern Neolithic agriculture, and the modern-day domesticated lentil germplasm is generally considered to form three broad adaptation groups: Mediterranean, South Asian and northern temperate, which correspond approximately to the major global production environments. Understanding the molecular basis of these adaptations is crucial to maximise efficiency of breeding programs. Here, we use a QTL approach to dissect the earliness that is characteristic of the South Asian pilosae ecotype, and that suits it to the typically short winter cropping season. We identified two loci, DTF6a and DTF6b, at which dominant alleles confer early flowering. We show that, although these loci can interact in an additive manner, DTF6a alone is sufficient to confer early flowering even in extremely short photoperiods. Comparisons with closely related legume species confirmed the presence of a conserved cluster of three FT orthologs among potential candidate genes in the region, and expression analysis in near-isogenic material showed that the early dtf6a allele is associated with a strong derepression of the FTa1 gene in particular. Analysis of sequence variation revealed the presence of a 7.4 kb deletion in the FTa1-FTa2 intergenic region in the pilosae parent, and a wide survey of over 400 accessions with diverse origin showed that the dtf6a allele is dominant in South Asia material. Collectively, these results contribute to understanding the molecular basis of global adaptation in lentil, and further emphasize the importance of this conserved genomic region for adaptation in temperate legumes generally.

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“…By changing this ratio in controlled growth chambers, we can simulate the effect of shading on plants while controlling for confounding effects such as competition for other resources. Results from our earlier lentil study ( Yuan et al, 2021 ) suggested potential roles for genes within the florigen gene family, several MADS-box transcription factors, and bHLH transcription factors, in regulating flowering time under such conditions in lentils. In this study, we used a holistic approach to examine the gene expression changes under different light qualities, as well as gene functionalities between the cultivated lentil and its wild relative, L. orientalis , to help better understand SAS in lentils.…”

Section: Discussionmentioning

confidence: 99%

RNA-Seq and Gene Ontology Analysis Reveal Differences Associated With Low R/FR-Induced Shade Responses in Cultivated Lentil and a Wild Relative

Yuan

Caron²,

Vandenberg³

et al. 2022

Front. Genet.

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Lentil is an important pulse crop not only because of its high nutrient value but also because of its ecological advantage in a sustainable agricultural system. Our previous work showed that the cultivated lentil and wild lentil germplasm respond differently to light environments, especially to low R/FR-induced shade conditions. Little is known about how cultivated and wild lentils respond to shade at the level of gene expression and function. In this study, transcriptomic profiling of a cultivated lentil (Lupa, L. culinaris) and a wild lentil (BGE 016880, L. orientalis) at several growth stages is presented. De novo transcriptomes were assembled for both genotypes, and differential gene expression analysis and gene ontology enrichment analysis were performed. The transcriptomic resources generated in this study provide fundamental information regarding biological processes and genes associated with shade responses in lentils. BGE 016880 and Lupa shared a high similarity in their transcriptomes; however, differential gene expression profiles were not consistent between these two genotypes. The wild lentil BGE 016880 had more differentially expressed genes than the cultivated lentil Lupa. Upregulation of genes involved in gibberellin, brassinosteroid, and auxin synthesis and signaling pathways, as well as cell wall modification, in both genotypes explains their similarity in stem elongation response under the shade. Genes involved in jasmonic acid and flavonoid biosynthesis pathways were downregulated in BGE 016880 only, and biological processes involved in defense responses were significantly enriched in the wild lentil BGE 016880 only. Downregulation of WRKY and MYB transcription factors could contribute to the reduced defense response in BGE 016880 but not in Lupa under shade conditions. A better understanding of shade responses of pulse crop species and their wild relatives will play an important role in developing genetic strategies for crop improvement in response to changes in light environments.

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Genetic and gene expression analysis of flowering time regulation by light quality in lentil

Cited by 16 publications

References 83 publications

Genetic analysis of early phenology in lentil identifies distinct loci controlling component traits

Genetic analysis of early phenology in lentil identifies distinct loci controlling component traits

Genetic analysis of early phenology in lentil identifies distinct loci controlling component traits

RNA-Seq and Gene Ontology Analysis Reveal Differences Associated With Low R/FR-Induced Shade Responses in Cultivated Lentil and a Wild Relative

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