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17 pages, 2144 KiB

Open AccessArticle

Use of High Resolution Spatiotemporal Gene Expression Data to Uncover Novel Tissue-Specific Promoters in Tomato

by Lulu Chen, Yuhang Li, Yuting Wang, Wenzhen Li, Xuechao Feng and Lingxia Zhao

Agriculture 2021, 11(12), 1195; https://doi.org/10.3390/agriculture11121195 - 27 Nov 2021

Cited by 5 | Viewed by 3550

Abstract

Genetic modification can be an effective strategy for improving the agronomic traits of tomato (Solanum lycopersicum) to meet demands for yield, quality, functional components, and stress tolerance. However, limited numbers of available tissue-specific promoters represent a bottleneck for the design and [...] Read more.

Genetic modification can be an effective strategy for improving the agronomic traits of tomato (Solanum lycopersicum) to meet demands for yield, quality, functional components, and stress tolerance. However, limited numbers of available tissue-specific promoters represent a bottleneck for the design and production of transgenic plants. In the current study, a total of 25 unigenes were collected from an RNA-sequence dataset based on their annotation as being exclusively expressed in five type of tissues of tomato pericarp (outer and inner epidermis, collenchyma, parenchyma, and vascular tissues), and every five unigenes, was respectively selected from each tissue based on transcription expression. The 3-kb 5′ upstream region of each unigene was identified from the tomato genome sequence (SL2.50) using annotated unigene sequences, and the promoter sequences were further analyzed. The results showed an enrichment in T/A (T/A > 70%) in the promoter regions. A total of 15 putative tissue-/organ-specific promoters were identified and analyzed by real-time (RT) quantitative (q) PCR analysis, of which six demonstrated stronger activity than widely used tissue-specific tomato promoters. These results demonstrate how high spatiotemporal and high throughput gene expression data can provide a powerful means of identifying spatially targeted promoters in plants. Full article

(This article belongs to the Special Issue Breeding and Genetics of Horticultural Crops)

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12 pages, 1745 KiB

Open AccessArticle

QTL Analysis for Chlorophyll Content in Strawberry (Fragaria × ananassa Duch.) Leaves

by Muhammad Irfan Siddique, Koeun Han, Jieun Lee, Eun Su Lee, Ye-Rin Lee, Hye-Eun Lee, Sun Yi Lee and Do-Sun Kim

Agriculture 2021, 11(11), 1163; https://doi.org/10.3390/agriculture11111163 - 18 Nov 2021

Cited by 5 | Viewed by 3555

Abstract

Chlorophyll is an important factor facilitating plants to capture, allocate and transforms light energy and plays a major role in yield formation. Strawberry is one of the most important fruit crops worldwide. Breeding strawberry for better light utilization by improving photosynthetic efficiency can [...] Read more.

Chlorophyll is an important factor facilitating plants to capture, allocate and transforms light energy and plays a major role in yield formation. Strawberry is one of the most important fruit crops worldwide. Breeding strawberry for better light utilization by improving photosynthetic efficiency can improve the yield potential. In strawberry, genetic studies have been done for several traits, but no reports on the genetic mapping of chlorophyll content in leaves. In the present study, we used two independent F₂ mapping populations (BS-F₂ and BC-F₂) and, Axiom 35 K strawberry chip and genotyping-by-sequencing derived single nucleotide polymorphisms based linkage maps to identify the quantitative trait loci (QTLs) controlling leaf chlorophyll content. SPAD values were used to estimate the leaf chlorophyll content of parental lines and F₂ populations. A total of seven QTLs, including major and minor effects, common and specific to populations, were identified across the strawberry genome explaining phenotypic variation (R²) ranging from 1.4 to 26.4%. Candidate genes associated with the photosynthesis and chlorophyll content were inferred in commonly detected QTLs. This work thus provides not only information for novel loci controlling chlorophyll content in strawberry leaves but also forms the basis for future marker assisted breeding in strawberry to select the plants for required chlorophyll content. Full article

(This article belongs to the Special Issue Breeding and Genetics of Horticultural Crops)

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12 pages, 1533 KiB

Open AccessArticle

Breeding Capsicum chinense Lines with High Levels of Capsaicinoids and Capsinoids in the Fruit

by Siyoung Jang, Minjeong Park, Do-Gyeong Lee, Jung-Hyun Lim, Ji-Won Jung and Byoung-Cheorl Kang

Agriculture 2021, 11(9), 819; https://doi.org/10.3390/agriculture11090819 - 28 Aug 2021

Cited by 13 | Viewed by 3612

Abstract

Capsaicinoids, which cause a hot sensation when eaten, are uniquely present in pepper (Capsicum sp.) and are biosynthesized by combining vanillyl amine with branched fatty acids. A mutation in the gene encoding putative aminotransferase (pAMT)—the enzyme that normally biosynthesizes the capsaicinoid precursor [...] Read more.

Capsaicinoids, which cause a hot sensation when eaten, are uniquely present in pepper (Capsicum sp.) and are biosynthesized by combining vanillyl amine with branched fatty acids. A mutation in the gene encoding putative aminotransferase (pAMT)—the enzyme that normally biosynthesizes the capsaicinoid precursor vanillyl amine—leads instead to the biosynthesis of vanillyl alcohol, which combines with branched fatty acids to form capsinoids. Here, we report a method for increasing the capsaicinoid and capsinoid contents using quantitative trait locus (QTL) alleles involved in capsaicinoid biosynthesis in the pericarps of extremely spicy peppers. QTLs for capsinoid contents were detected on chromosome 6 and 10 using an F₂ population from ‘SNU11–001’ and ‘Bhut Jolokia (BJ)’ (‘SJ’). ‘SNU11–001’ contains high capsinoid contents and ‘BJ’ contains high capsaicinoid contents in both the placenta and pericarp. These QTLs overlapped QTL regions associated with pungency in the pericarp. ‘BJ’ was crossed also with ‘Habanero’ (‘HB’), which contains capsaicinoids mainly in the placenta, and the resulting (‘HJ’) F₂ and F₃ offspring with ‘BJ’ genotypes were selected based on QTL markers and the pericarp pungency phenotype. Similarly, F₂ and F₃ offspring with high capsinoid contents in the pericarp were selected in ‘SJ’ with reference to ‘BJ’ genotypes at the QTLs. Through continuous self-pollination, ‘SJ’ and ‘BJ’ lines with high capsinoid and capsaicinoid contents, respectively, in both the placenta and pericarp were developed. This study is the first to show that lines containing high levels of capsinoids and capsaicinoids can be bred using pericarp capsaicinoid biosynthesis genes. Full article

(This article belongs to the Special Issue Breeding and Genetics of Horticultural Crops)

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10 pages, 237 KiB

Open AccessArticle

Using Simple Sequence Repeats in 9 Brassica Complex Species to Assess Hypertrophic Curd Induction

by Simone Treccarichi, Cornelia Di Gaetano, Fulvio Di Stefano, Mauro Gasparini and Ferdinando Branca

Agriculture 2021, 11(7), 622; https://doi.org/10.3390/agriculture11070622 - 1 Jul 2021

Cited by 10 | Viewed by 2160

Abstract

Five Simple Sequence Repeats (SSRs) were used to assess the relationship between inflorescence characteristics and their allelic variation in 53 Brassica oleracea and Brassica wild relatives (n = 9). Curd morphometric traits, such as weight (CW), height (CH), diameter (CD1), shape (CS) [...] Read more.

Five Simple Sequence Repeats (SSRs) were used to assess the relationship between inflorescence characteristics and their allelic variation in 53 Brassica oleracea and Brassica wild relatives (n = 9). Curd morphometric traits, such as weight (CW), height (CH), diameter (CD1), shape (CS) inflorescence curvature angle (CA), and its curd stem diameter (CD2), were measured. The aim of the work was to analyze the relationships among the allelic patterns of the SSRs primers utilized, and their status of homo or heterozygosity registered at each locus, as well as the inflorescence morphometric traits in order to individuate genomic regions stimulating the hypertrophy of this reproductive organ. The relationships found explain the diversity among B. oleracea complex species (n = 9) for the inflorescence size and structure, allowing important time reduction during the breeding process by crossing wild species, transferring useful resistance, and organoleptic and nutraceutical traits. The five SSRs loci were BoABI1, BoAP1, BoPLD1, BoTHL1, and PBCGSSRBo39. According to the allelic variation ascertained, we evaluated the heterozygosity index (H) for each SSR above cited. The results showed a significant interaction between the H index of the BoPLD1 gene and the inflorescence characteristics, summarized by the First Principal Component (PC1) (p-value = 0.0244); we ascertained a negative correlation between the H index and inflorescence characteristics, namely CW, CH, CD1, CD2, CA. The homozygosity BoPLD1 alelles, indicated by the H index, affect the inflorescence characteristics and broccoli and cauliflower yields. Full article

(This article belongs to the Special Issue Breeding and Genetics of Horticultural Crops)

22 pages, 5938 KiB

Open AccessFeature PaperEditor’s ChoiceArticle

An Eleven-Year Survey on Field Disease Susceptibility of Citrus Accessions to Colletotrichum and Alternaria Species

by Alessandro Vitale, Dalia Aiello, Antonino Azzaro, Vladimiro Guarnaccia and Giancarlo Polizzi

Agriculture 2021, 11(6), 536; https://doi.org/10.3390/agriculture11060536 - 10 Jun 2021

Cited by 18 | Viewed by 7439

Abstract

In the past decade Colletotrichum gloeosporioides, C. karstii, and Alternaria alternata represent emerging fungal pathogens on citrus in the Mediterranean basin. Selection of tolerant Citrus germplasm offers evaluable long-term solution and should be considered as promising alternative to limit synthetic fungicide [...] Read more.

In the past decade Colletotrichum gloeosporioides, C. karstii, and Alternaria alternata represent emerging fungal pathogens on citrus in the Mediterranean basin. Selection of tolerant Citrus germplasm offers evaluable long-term solution and should be considered as promising alternative to limit synthetic fungicide application to manage Alternaria and Colletotrichum infections in Citrus groves. In this study, the high variability of pre-harvest disease symptoms among 37 Citrus accessions was investigated in Italy in the most representative Sicilian production districts covering 1500 ha and including 20 homogeneous areas over an eleven-year survey period (2010–2020). Early fruit drop, brown spot, and anthracnose on fruit and leaves, pre-harvest fruit drop, and twig blight and defoliation associated to Alternaria and Colletotrichum spp. were identified on oranges, mandarins, and lemons. Comprehensively, first extensive data obtained herein on field susceptibility within “Tarocco” blood orange group to above disease symptoms clearly indicate as “Tarocco Nucellare 57-1E-1,” “Tarocco Tapi,” “Tarocco Sant’Alfio,” and “Tarocco Catania” accessions should be preferred to remaining Tarocco ones. A broad degree of tolerance or susceptibility was also observed within other Citrus group as it happens for tolerant lemon “Femminello Zagara Bianca,” thus demonstrating a putative resource for further studies to employ in a breeding program for genetic improvement of Citrus. Full article

(This article belongs to the Special Issue Breeding and Genetics of Horticultural Crops)

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21 pages, 3141 KiB

Open AccessEditor’s ChoiceArticle

Segregation Distortion for Male Parents in High Density Genetic Maps from Reciprocal Crosses between Two Self-Incompatible Cultivars Confirms a Gametophytic System for Self-Incompatibility in Citrus

by Patrick Ollitrault, Dalel Ahmed, Gilles Costantino, Jean-Charles Evrard, Celine Cardi, Pierre Mournet, Aude Perdereau and Yann Froelicher

Agriculture 2021, 11(5), 379; https://doi.org/10.3390/agriculture11050379 - 23 Apr 2021

Cited by 16 | Viewed by 4112

Abstract

Self-incompatibility is an important evolutionary feature in angiosperms and has major implications for breeding strategies in horticultural crops. In citrus, when coupled with parthenocarpy, it enables the production of seedless fruits in a mono-varietal orchard. A gametophytic incompatibility system with one S locus [...] Read more.

Self-incompatibility is an important evolutionary feature in angiosperms and has major implications for breeding strategies in horticultural crops. In citrus, when coupled with parthenocarpy, it enables the production of seedless fruits in a mono-varietal orchard. A gametophytic incompatibility system with one S locus was proposed for citrus, but its molecular mechanisms remain the subject of debate. The objective of this work was to locate the S locus by the analyzing segregation distortion in reciprocal crosses of two self-incompatible citrus sharing one self-incompatible allele and to compare this location with previously published models. High density genetic maps of ‘Fortune’ mandarin and ‘Ellendale tangor’ with, respectively, 2164 SNP and 1467 SNP markers, were constructed using genotyping by sequencing data. They are highly syntenic and collinear with the clementine genome. Complete rejection of one allele was only observed in male segregation in the two parents and in only one genomic area, at the beginning of chromosome 7 of the clementine reference genome. Haplotype data in the area surrounding the theoretical S locus were in agreement with previously proposed S genotypes. Overall, our results are in full agreement with the recently proposed gametophytic S-RNase system with the S locus at the beginning of chromosome 7 of the clementine reference genome. Full article

(This article belongs to the Special Issue Breeding and Genetics of Horticultural Crops)

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11 pages, 1713 KiB

Open AccessArticle

Rootstock Affects Floral Induction in Citrus Engaging the Expression of the FLOWERING LOCUS T (CiFT)

by Stefania Bennici, Giuseppina Las Casas, Gaetano Distefano, Alessandra Gentile, Giuseppe Lana, Mario Di Guardo, Elisabetta Nicolosi, Stefano La Malfa and Alberto Continella

Agriculture 2021, 11(2), 140; https://doi.org/10.3390/agriculture11020140 - 8 Feb 2021

Cited by 11 | Viewed by 3331

Abstract

In Citrus, flower induction represents the transition from vegetative to reproductive growth. The regulation of flower induction is mainly triggered by exposure to low temperatures and water-deficit stress, which activates the signaling cascade leading to an increased expression of the citrus orthologs [...] Read more.

In Citrus, flower induction represents the transition from vegetative to reproductive growth. The regulation of flower induction is mainly triggered by exposure to low temperatures and water-deficit stress, which activates the signaling cascade leading to an increased expression of the citrus orthologs of the FLOWERING LOCUS T (CiFT). In this study, the relationship between rootstock and flower induction under Mediterranean field conditions was investigated by monitoring the expression levels of the floral promoter CiFT2 in leaves of the pigmented sweet orange “Tarocco Scirè” grafted onto “C35” citrange and “Swingle” citrumelo rootstocks. The latter two are known to confer, respectively, high and low yield efficiency to the scion. In both rootstock/scion combinations, CiFT2 showed a seasonal expression with a peak during the inductive period in January triggered by cold temperature. The “Tarocco Scirè”/”C35” citrange combination showed the highest expression levels for CiFT2; this increased expression was correlated with yield and a higher number of flowers in the following spring, suggesting a significant effect of rootstocks on flower induction mediated by the overexpression of the CiFT2 gene. Full article

(This article belongs to the Special Issue Breeding and Genetics of Horticultural Crops)

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Review

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21 pages, 1978 KiB

Open AccessReview

Breeding for Nutritional and Organoleptic Quality in Vegetable Crops: The Case of Tomato and Cauliflower

by Alessandro Natalini, Nazzareno Acciarri and Teodoro Cardi

Agriculture 2021, 11(7), 606; https://doi.org/10.3390/agriculture11070606 - 29 Jun 2021

Cited by 18 | Viewed by 8225

Abstract

Due to novel and more demanding consumers’ requirements, breeding of vegetable crops confronts new challenges to improve the nutritional level and overall appearance of produce. Such objectives are not easy to achieve considering the complex genetic and physiological bases. Overtime, plant breeders relied [...] Read more.

Due to novel and more demanding consumers’ requirements, breeding of vegetable crops confronts new challenges to improve the nutritional level and overall appearance of produce. Such objectives are not easy to achieve considering the complex genetic and physiological bases. Overtime, plant breeders relied on a number of technologies and methods to achieve ever changing targets. F1 hybrid seed production allowed the exploitation of heterosis and facilitated the combination of resistance and other useful genes in a uniform outperforming variety. Mutagenesis and tissue culture techniques permitted to induce novel variation, overcome crossing barriers, and speed up the achievement of true-breeding lines. Marker-assisted selection was one of the milestones in fastening selection, starting from the early ’90s in almost all seed companies. Only recently, however, are novel omics tools and genome editing being used as cutting-edge techniques to face old and new challenges in vegetable crops, with the potential to increase the qualitative value of crop cultivation and solve malnutrition in 10 billion people over the next 30 years. In this manuscript, the evolution of breeding approaches in vegetable crops for quality is reviewed, reporting case studies in tomato (Solanum lycopersicum L.) and cauliflower (Brassica oleracea var. botrytis L.) as model systems for fleshy fruit and floral edible parts, respectively. Full article

(This article belongs to the Special Issue Breeding and Genetics of Horticultural Crops)

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