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15 pages, 2322 KiB

Open AccessArticle

Detection of Transcription Factors Related to Axillary Bud Development after Exposure to Cold Conditions in Hexaploid Chrysanthemum morifolium Using Arabidopsis Information

by Tsuyoshi Tanaka and Katsutomo Sasaki

Plants 2023, 12(17), 3122; https://doi.org/10.3390/plants12173122 - 30 Aug 2023

Viewed by 1033

Abstract

Chrysanthemum is one of the most commercially used ornamental flowering plants in the world. As chrysanthemum is self-incompatible, the propagation of identical varieties is carried out through cuttings rather than through seed. Axillary bud development can be controlled by changing the temperature; for [...] Read more.

Chrysanthemum is one of the most commercially used ornamental flowering plants in the world. As chrysanthemum is self-incompatible, the propagation of identical varieties is carried out through cuttings rather than through seed. Axillary bud development can be controlled by changing the temperature; for instance, axillary bud development in some varieties is suppressed at high temperatures. In this study, we focused on the simultaneous axillary bud growth from multiple lines of chrysanthemum upon changing conditions from low to normal temperature. Transcriptome analysis was conducted on the Chrysanthemum morifolium cultivar ’Jinba’ to identify the important genes for axillary bud development seen when moved from low-temperature treatment to normal cultivation temperature. We performed RNA-Seq analysis on plants after cold conditions in two-day time-course experiments. Under these settings, we constructed a transcriptome of 415,923 C. morifolium and extracted 7357 differentially expressed genes. Our understanding of Arabidopsis axillary meristem development and growth showed that at least 101 genes in our dataset were homologous to transcription factors involved in the biological process. In addition, six genes exhibited statistically significant variations in expression throughout conditions. We hypothesized that these genes were involved in the formation of axillary buds in C. morifolium after cold conditions. Full article

(This article belongs to the Special Issue Molecular Markers and Molecular Breeding in Horticultural Plants)

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12 pages, 1067 KiB

Open AccessArticle

Development and Application of a Cleaved Amplified Polymorphic Sequence Marker (Phyto) Linked to the Pc5.1 Locus Conferring Resistance to Phytophthora capsici in Pepper (Capsicum annuum L.)

by Giacomo Bongiorno, Annamaria Di Noia, Simona Ciancaleoni, Gianpiero Marconi, Vincenzo Cassibba and Emidio Albertini

Plants 2023, 12(15), 2757; https://doi.org/10.3390/plants12152757 - 25 Jul 2023

Cited by 1 | Viewed by 1051

Abstract

Phytophthora capsici causes destructive disease in several crop species, including pepper (Capsicum annuum L.). Resistance in this species is physiologically and genetically complex due to many P. capsici virulence phenotypes and different QTLs and R genes among the identified resistance sources. Several [...] Read more.

Phytophthora capsici causes destructive disease in several crop species, including pepper (Capsicum annuum L.). Resistance in this species is physiologically and genetically complex due to many P. capsici virulence phenotypes and different QTLs and R genes among the identified resistance sources. Several primer pairs were designed to follow an SNP (G/A) within the CA_011264 locus linked to the Pc5.1 locus. All primer pairs were designed on DNA sequences derived from CaDMR1, a homoserine kinase (HSK), which is a gene candidate responsible for the major QTL on chromosome P5 for resistance to P. capsici. A panel of 69 pepper genotypes from the Southern Seed germplasm collection was used to screen the primer pairs designed. Of these, two primers (Phyto_for_2 and Phyto_rev_2) surrounding the SNP proved successful in discriminating susceptible and resistant genotypes when combined with a restriction enzyme (BtgI). This new marker (called Phyto) worked as expected in all genotypes tested, proving to be an excellent candidate for marker-assisted selection in breeding programs aimed at introgressing the resistant locus into pure lines. Full article

(This article belongs to the Special Issue Molecular Markers and Molecular Breeding in Horticultural Plants)

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17 pages, 16321 KiB

Open AccessArticle

A Chromosome-Level Genome of ‘Xiaobaixing’ (Prunus armeniaca L.) Provides Clues to Its Domestication and Identification of Key bHLH Genes in Amygdalin Biosynthesis

by Ling Guo, Fangjie Xie, Xue Huang and Zhengrong Luo

Plants 2023, 12(15), 2756; https://doi.org/10.3390/plants12152756 - 25 Jul 2023

Cited by 1 | Viewed by 1548

Abstract

Apricot is a widely cultivated fruit tree of the drupe family, and its sweet/bitter kernel traits are important indicators of the quality and merchantability of apricots. The sweetness/bitterness traits were mainly determined by amygdalin content. However, the lack of high-quality genomes has limited [...] Read more.

Apricot is a widely cultivated fruit tree of the drupe family, and its sweet/bitter kernel traits are important indicators of the quality and merchantability of apricots. The sweetness/bitterness traits were mainly determined by amygdalin content. However, the lack of high-quality genomes has limited insight into the traits. In this study, a high-quality genome of ‘Xiaobaixing’ was obtained by using single-molecule sequencing and chromosome-conformation capture techniques, with eight chromosomes of 0.21 Gb in length and 52.80% repetitive sequences. A total of 29,157 protein-coding genes were predicted with contigs N50 = 3.56 Mb and scaffold N50 = 26.73 Mb. Construction of phylogenetic trees of 15 species of Rosaceae fruit trees, with ‘Xiaobaixing’ differentiated by 5.3 Ma as the closest relative to ‘Yinxiangbai’. GO functional annotation and KEGG enrichment analysis identified 227 specific gene families to ‘Xiaobaixing’, with 569 expansion-gene families and 1316 contraction-gene families, including the significant expansion of phenylalanine N-monooxygenase and β-glucosidase genes associated with amygdalin synthesis, significant contraction of wild black cherry glucoside β-glucosidase genes, amygdalin β-glucosidase genes, and β-glucosidase genes, and significant enrichment of positively selected genes in the cyanogenic amino acid metabolic pathway. The 88 bHLH genes were identified in the genome of ‘Xiaobaixing’, and ParbHLH66 (rna-Par24659.1) was found to be a key gene for the identification of sweet/bitter kernels of apricots. The amino acid sequence encoded by its gene is highly conserved in the species of Prunus mume, Prunus dulcis, Prunus persica, and Prunus avium and may be participating in the regulation of amygdalin biosynthesis, which provides a theoretical foundation for the molecular identification of sweet/bitter kernels of apricots. Full article

(This article belongs to the Special Issue Molecular Markers and Molecular Breeding in Horticultural Plants)

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16 pages, 2919 KiB

Open AccessArticle

A Genome-Wide Association Study Reveals Region Associated with Seed Protein Content in Cowpea

by Yilin Chen, Haizheng Xiong, Waltram Ravelombola, Gehendra Bhattarai, Casey Barickman, Ibtisam Alatawi, Theresa Makawa Phiri, Kenani Chiwina, Beiquan Mou, Shyam Tallury and Ainong Shi

Plants 2023, 12(14), 2705; https://doi.org/10.3390/plants12142705 - 20 Jul 2023

Cited by 4 | Viewed by 1947

Abstract

Cowpea (Vigna unguiculata L. Walp., 2n = 2x = 22) is a protein-rich crop that complements staple cereals for humans and serves as fodder for livestock. It is widely grown in Africa and other developing countries as the primary source [...] Read more.

Cowpea (Vigna unguiculata L. Walp., 2n = 2x = 22) is a protein-rich crop that complements staple cereals for humans and serves as fodder for livestock. It is widely grown in Africa and other developing countries as the primary source of protein in the diet; therefore, it is necessary to identify the protein-related loci to improve cowpea breeding. In the current study, we conducted a genome-wide association study (GWAS) on 161 cowpea accessions (151 USDA germplasm plus 10 Arkansas breeding lines) with a wide range of seed protein contents (21.8~28.9%) with 110,155 high-quality whole-genome single-nucleotide polymorphisms (SNPs) to identify markers associated with protein content, then performed genomic prediction (GP) for future breeding. A total of seven significant SNP markers were identified using five GWAS models (single-marker regression (SMR), the general linear model (GLM), Mixed Linear Model (MLM), Fixed and Random Model Circulating Probability Unification (FarmCPU), and Bayesian-information and Linkage-disequilibrium Iteratively Nested Keyway (BLINK), which are located at the same locus on chromosome 8 for seed protein content. This locus was associated with the gene Vigun08g039200, which was annotated as the protein of the thioredoxin superfamily, playing a critical function for protein content increase and nutritional quality improvement. In this study, a genomic prediction (GP) approach was employed to assess the accuracy of predicting seed protein content in cowpea. The GP was conducted using cross-prediction with five models, namely ridge regression best linear unbiased prediction (rrBLUP), Bayesian ridge regression (BRR), Bayesian A (BA), Bayesian B (BB), and Bayesian least absolute shrinkage and selection operator (BL), applied to seven random whole genome marker sets with different densities (10 k, 5 k, 2 k, 1 k, 500, 200, and 7), as well as significant markers identified through GWAS. The accuracies of the GP varied between 42.9% and 52.1% across the seven SNPs considered, depending on the model used. These findings not only have the potential to expedite the breeding cycle through early prediction of individual performance prior to phenotyping, but also offer practical implications for cowpea breeding programs striving to enhance seed protein content and nutritional quality. Full article

(This article belongs to the Special Issue Molecular Markers and Molecular Breeding in Horticultural Plants)

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15 pages, 751 KiB

Open AccessArticle

Population Genetic Analysis in Persimmons (Diospyros kaki Thunb.) Based on Genome-Wide Single-Nucleotide Polymorphisms

by Seoyeon Park, Ye-Ok Park and Younghoon Park

Plants 2023, 12(11), 2097; https://doi.org/10.3390/plants12112097 - 24 May 2023

Cited by 1 | Viewed by 1282

Abstract

This study investigated the genetic diversity and population structure of a persimmon (Diospyros kaki Thunb., 2n = 6x = 90) collection in South Korea by evaluating 9751 genome-wide single-nucleotide polymorphisms (SNPs) detected using genotyping-by-sequencing in 93 cultivars. The results of neighbor-joining clustering, [...] Read more.

This study investigated the genetic diversity and population structure of a persimmon (Diospyros kaki Thunb., 2n = 6x = 90) collection in South Korea by evaluating 9751 genome-wide single-nucleotide polymorphisms (SNPs) detected using genotyping-by-sequencing in 93 cultivars. The results of neighbor-joining clustering, principal component analysis, and STRUCTURE analysis based on SNPs indicated clear separation between cultivar groups (pollination-constant nonastringent (PCNA, 40 cultivars), pollination-constant astringent (PCA, 19), pollination-variant nonastringent (PVNA, 23), and the pollination-variant astringent type (PVA, 9)) based on the astringency types, while separation between PVA and PVNA-type cultivars was unclear. Population genetic diversity based on SNPs showed that the proportions of polymorphic SNPs within each group ranged from 99.01% (PVNA) to 94.08% (PVA), and the PVNA group exhibited the highest genetic diversity (He = 3.86 and uHe = 0.397). F (fixation index) values were low ranging from −0.024 (PVA) to 0.176 (PCA) with an average of 0.089, indicating a deficiency of heterozygosity. Analysis of molecular variance (AMOVA) and Fst among cultivar groups indicated that variation within individuals was higher than that among the groups. Pairwise Fst values among the groups ranged from 0.01566 (between PVA and PVNA) to 0.09416 (between PCA and PCNA), indicating a low level of cultivar type differentiation. These findings highlight the potential application of biallelic SNPs in population genetics studies of allopolyploids species and provide valuable insights that may have significant implications for breeding and cultivar identification in persimmon. Full article

(This article belongs to the Special Issue Molecular Markers and Molecular Breeding in Horticultural Plants)

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18 pages, 2126 KiB

Open AccessArticle

White Lupin Adaptation to Moderately Calcareous Soils: Phenotypic Variation and Genome-Enabled Prediction

by Paolo Annicchiarico, Abco J. de Buck, Dimitrios N. Vlachostergios, Dennis Heupink, Avraam Koskosidis, Nelson Nazzicari and Margherita Crosta

Plants 2023, 12(5), 1139; https://doi.org/10.3390/plants12051139 - 2 Mar 2023

Cited by 1 | Viewed by 1606

Abstract

White lupin is a promising high-protein crop, the cultivation of which is limited by a lack of adaptation to soils that are even just mildly calcareous. This study aimed to assess the phenotypic variation, the trait architecture based on a GWAS, and the [...] Read more.

White lupin is a promising high-protein crop, the cultivation of which is limited by a lack of adaptation to soils that are even just mildly calcareous. This study aimed to assess the phenotypic variation, the trait architecture based on a GWAS, and the predictive ability of genome-enabled models for grain yield and contributing traits of a genetically-broad population of 140 lines grown in an autumn-sown environment of Greece (Larissa) and a spring-sown environment of the Netherlands (Ens) that featured moderately calcareous and alkaline soils. We found large genotype × environment interaction and modest or nil genetic correlation for line responses across locations for grain yield, a lime susceptibility score, and other traits, with the exception of individual seed weight and plant height. The GWAS identified significant SNP markers associated with various traits that were markedly inconsistent across locations, while providing direct or indirect evidence for widespread polygenic trait control. Genomic selection proved to be a feasible strategy, owing to a moderate predictive ability for yield and lime susceptibility in Larissa (the site featuring greater lime soil stress). Other supporting results for breeding programs where the identification of a candidate gene for lime tolerance and the high reliability of genome-enabled predictions for individual seed weight. Full article

(This article belongs to the Special Issue Molecular Markers and Molecular Breeding in Horticultural Plants)

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14 pages, 2227 KiB

Open AccessArticle

A Genome-Wide Association Study and Genomic Prediction for Fiber and Sucrose Contents in a Mapping Population of LCP 85-384 Sugarcane

by Haizheng Xiong, Yilin Chen, Yong-Bao Pan and Ainong Shi

Plants 2023, 12(5), 1041; https://doi.org/10.3390/plants12051041 - 24 Feb 2023

Cited by 2 | Viewed by 1769

Abstract

Sugarcane (Saccharum spp. hybrids) is an economically important crop for both sugar and biofuel industries. Fiber and sucrose contents are the two most critical quantitative traits in sugarcane breeding that require multiple-year and multiple-location evaluations. Marker-assisted selection (MAS) could significantly reduce the [...] Read more.

Sugarcane (Saccharum spp. hybrids) is an economically important crop for both sugar and biofuel industries. Fiber and sucrose contents are the two most critical quantitative traits in sugarcane breeding that require multiple-year and multiple-location evaluations. Marker-assisted selection (MAS) could significantly reduce the time and cost of developing new sugarcane varieties. The objectives of this study were to conduct a genome-wide association study (GWAS) to identify DNA markers associated with fiber and sucrose contents and to perform genomic prediction (GP) for the two traits. Fiber and sucrose data were collected from 237 self-pollinated progenies of LCP 85-384, the most popular Louisiana sugarcane cultivar from 1999 to 2007. The GWAS was performed using 1310 polymorphic DNA marker alleles with three models of TASSEL 5, single marker regression (SMR), general linear model (GLM) and mixed linear model (MLM), and the fixed and random model circulating probability unification (FarmCPU) of R package. The results showed that 13 and 9 markers were associated with fiber and sucrose contents, respectively. The GP was performed by cross-prediction with five models, ridge regression best linear unbiased prediction (rrBLUP), Bayesian ridge regression (BRR), Bayesian A (BA), Bayesian B (BB) and Bayesian least absolute shrinkage and selection operator (BL). The accuracy of GP varied from 55.8% to 58.9% for fiber content and 54.6% to 57.2% for sucrose content. Upon validation, these markers can be applied in MAS and genomic selection (GS) to select superior sugarcane with good fiber and high sucrose contents. Full article

(This article belongs to the Special Issue Molecular Markers and Molecular Breeding in Horticultural Plants)

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16 pages, 2255 KiB

Open AccessArticle

Identification of Candidate Genes for Rind Color and Bloom Formation in Watermelon Fruits Based on a Quantitative Trait Locus-Seq

by Siyoung Lee, Gaeun Jang, Yunseo Choi, Girim Park, Seoyeon Park, Gibeom Kwon, Byoungil Je and Younghoon Park

Plants 2022, 11(20), 2739; https://doi.org/10.3390/plants11202739 - 17 Oct 2022

Cited by 4 | Viewed by 2117

Abstract

Watermelon fruit rind color (RC) and bloom formation (BF) affect product value and consumer preference. However, information on the candidate gene(s) for additional loci involved in dark green (DG) RC and the genetic control of BF and its major chemical components is lacking. [...] Read more.

Watermelon fruit rind color (RC) and bloom formation (BF) affect product value and consumer preference. However, information on the candidate gene(s) for additional loci involved in dark green (DG) RC and the genetic control of BF and its major chemical components is lacking. Therefore, this study aimed to identify loci controlling RC and BF using QTL-seq of the F₂ population derived by crossing ‘FD061129’ with light-green rind and bloom and ‘SIT55616RN’ with DG rind and bloomless. Phenotypic evaluation of the F₁ and 219 F₂ plants indicated the genetic control of two complementary dominant loci, G₁ and G₂, for DG and a dominant locus, Bf, for BF. QTL-seq identified a genomic region on Chr.6 for G₁, Chr.8 for G₂, and Chr.1 for Bf. G₁ and G₂ helped determine RC with possible environmental effects. Chlorophyll a-b binding protein gene-based CAPS (RC-m5) at G₁ matched the highest with the RC phenotype. In the 1.4 cM Bf map interval, two additional gene-based CAPS markers were designed, and the CAPS for a nonsynonymous SNP in Cla97C01G020050, encoding a CSC1-like protein, cosegregated with the BF trait in 219 F₂ plants. Bloom powder showed a high Ca²⁺ concentration (16,358 mg·kg⁻¹), indicating that the CSC1-like protein gene is possibly responsible for BF. Our findings provide valuable information for marker-assisted selection for RC and BF and insights into the functional characterization of genes governing these watermelon-fruit-related traits. Full article

(This article belongs to the Special Issue Molecular Markers and Molecular Breeding in Horticultural Plants)

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9 pages, 1167 KiB

Open AccessFeature PaperArticle

Assessment of Temperature-Independent Resistance against Bacterial Wilt Using Major QTL in Cultivated Tomato (Solanum lycopersicum L.)

by Jeyun Yeon, Ngoc Thi Le and Sung-Chur Sim

Plants 2022, 11(17), 2223; https://doi.org/10.3390/plants11172223 - 27 Aug 2022

Cited by 4 | Viewed by 1634

Abstract

Bacterial wilt (Ralstonia solanacearum) is a devastating disease of cultivated tomato resulting in severe yield loss. Since chemicals are often ineffective in controlling this soil-borne pathogen, quantitative trait loci (QTL) conferring host resistance have been extensively explored. In this study, we [...] Read more.

Bacterial wilt (Ralstonia solanacearum) is a devastating disease of cultivated tomato resulting in severe yield loss. Since chemicals are often ineffective in controlling this soil-borne pathogen, quantitative trait loci (QTL) conferring host resistance have been extensively explored. In this study, we investigated effects of ambient temperature and major QTL on bacterial wilt resistance in a collection of 50 tomato varieties. The five-week-old seedlings were inoculated using the race 1 (biovar 4 and phylotype I) strain of R. solanacearum and placed at growth chambers with three different temperatures (24 °C, 28 °C, and 36 °C). Disease severity was evaluated for seven days after inoculation using the 1–5 rating scales. Consistent bacterial wilt resistance was observed in 25 tomato varieties (R group) with the means of 1.16–1.44 for disease severity at all three temperatures. Similarly, 10 susceptible varieties with the means of 4.37–4.73 (S group) were temperature-independent. However, the other 15 varieties (R/S group) showed moderate levels of resistance at both 24 °C (1.84) and 28 °C (2.16), while they were highly susceptible with a mean of 4.20 at 36 °C. The temperature-dependent responses in the R/S group were supported by pairwise estimates of the Pearson correlation coefficients. Genotyping for three major QTL (Bwr-4, Bwr-6 and Bwr-12) found that 92% of varieties in the R group had ≥ two QTL and 40% of varieties in the R/S group had one or two QTL. This suggests that these QTL are important for stability of resistance against bacterial wilt at high ambient temperature. The resulting 25 varieties with temperature-independent resistance will be a useful resource to develop elite cultivars in tomato breeding programs. Full article

(This article belongs to the Special Issue Molecular Markers and Molecular Breeding in Horticultural Plants)

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