Mapping and Characterization QTLs for Phenological Traits in Seven Pedigree-connected Peach Families

Abstract BackgroundEnvironmental adaptation and expanding harvest seasons are primary goals of most peach [Prunus persica (L.) Batsch] breeding programs. Breeding perennial crops is a challenging task due to their long breeding cycles and large tree size. Pedigree-based analysis using pedigreed families followed by haplotype construction creates a platform for QTL and marker identification, validation, and the use of marker-assisted selection in breeding programs.ResultsPhenotypic data of seven F1 low to medium chill full-sib families were collected over two years at two locations and genotyped using the 9K SNP Illumina array. Three QTLs were discovered for bloom date (BD) and mapped on linkage group 1 (LG1) (172 – 182 cM), LG4 (48 – 54 cM), and LG7 (62 – 70 cM), explaining 17-54%, 11-55%, and 11-18% of the phenotypic variance, respectively. The QTL for ripening date (RD) and fruit development period (FDP) on LG4 was co-localized at the central part of LG4 (40 - 46 cM) and explained between 40-75% of the phenotypic variance. Haplotype analyses revealed SNP haplotypes and predictive SNP marker(s) associated with desired QTL alleles and the presence of multiple functional alleles with different effects for a single locus for RD and FDP.ConclusionsA multiple pedigree-linked families approach validated major QTLs for the three key phenological traits which were reported in previous studies across diverse materials, geographical distributions, and QTL mapping methods. Haplotype characterization of these genomic regions differentiates this study from the previous QTL studies. Our results will provide the peach breeder with the haplotypes for three BD QTLs and one RD/FDP QTL for the creation of predictive DNA-based molecular marker tests to select parents and/or seedlings that have desired QTL alleles and cull unwanted genotypes in early seedling stages.

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Mapping and characterization QTLs for phenological traits in seven pedigree-connected peach families

BMC Genomics ◽

10.1186/s12864-021-07483-8 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Zena J. Rawandoozi ◽

Timothy P. Hartmann ◽

Silvia Carpenedo ◽

Ksenija Gasic ◽

Cassia da Silva Linge ◽

...

Keyword(s):

Prunus Persica ◽

Phenotypic Variance ◽

Phenotypic Data ◽

Breeding Programs ◽

Large Tree ◽

Early Seedling ◽

Sib Families ◽

Functional Alleles ◽

Genomic Regions

Abstract Background Environmental adaptation and expanding harvest seasons are primary goals of most peach [Prunus persica (L.) Batsch] breeding programs. Breeding perennial crops is a challenging task due to their long breeding cycles and large tree size. Pedigree-based analysis using pedigreed families followed by haplotype construction creates a platform for QTL and marker identification, validation, and the use of marker-assisted selection in breeding programs. Results Phenotypic data of seven F1 low to medium chill full-sib families were collected over 2 years at two locations and genotyped using the 9 K SNP Illumina array. Three QTLs were discovered for bloom date (BD) and mapped on linkage group 1 (LG1) (172–182 cM), LG4 (48–54 cM), and LG7 (62–70 cM), explaining 17–54%, 11–55%, and 11–18% of the phenotypic variance, respectively. The QTL for ripening date (RD) and fruit development period (FDP) on LG4 was co-localized at the central part of LG4 (40–46 cM) and explained between 40 and 75% of the phenotypic variance. Haplotype analyses revealed SNP haplotypes and predictive SNP marker(s) associated with desired QTL alleles and the presence of multiple functional alleles with different effects for a single locus for RD and FDP. Conclusions A multiple pedigree-linked families approach validated major QTLs for the three key phenological traits which were reported in previous studies across diverse materials, geographical distributions, and QTL mapping methods. Haplotype characterization of these genomic regions differentiates this study from the previous QTL studies. Our results will provide the peach breeder with the haplotypes for three BD QTLs and one RD/FDP QTL to create predictive DNA-based molecular marker tests to select parents and/or seedlings that have desired QTL alleles and cull unwanted genotypes in early seedling stages.

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Characterization of the Common japonica-Originated Genomic Regions in the High Yielding Varieties Developed from Inter-Subspecific Crosses in Rice (Oryza sativa L.)

10.20944/preprints202004.0428.v1 ◽

2020 ◽

Author(s):

Jeonghwan Seo ◽

So-Myeong Lee ◽

Jae-Hyuk Han ◽

Na-Hyun Shin ◽

Yoon Kyung Lee ◽

...

Keyword(s):

Molecular Breeding ◽

Snp Markers ◽

Yield Potential ◽

Breeding Programs ◽

Wx Gene ◽

High Yielding Varieties ◽

Indica And Japonica Subspecies ◽

Genomic Regions ◽

Further Development

The inter-subspecific crossing between indica and japonica subspecies in rice have been utilized to improve yield potential in temperate rice. In this study, a comparative study of the genomic regions in the eight high yielding varieties (HYVs) was conducted with those of the four non-HYV varieties. NGS mapping on the Nipponbare reference genome identified a total of 14 common genomic regions of japonica-originated alleles. Interestingly, the HYVs shared the japonica-originated genomic regions on the nine chromosomes, although they were developed from different breeding programs. A panel of 94 varieties was classified into four varietal groups with the 39 SNP markers from 39 genes residing the japonica-originated genomic regions and 16 additional trait-specific SNPs. As expected, the japonica originated genomic regions were present only in JAP and HYV groups with exceptions for Chr4-1 and Chr4-2. The Wx gene located within Chr6-1 was present in HYV and JAP variety groups, while the yield-related genes were conserved as indica alleles in HYVs. The japonica-originated genomic regions and alleles shared by HYVs can be employed in molecular breeding programs for further development of HYVs in rice.

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SELECTION OF PEACH GENOTYPES FOR BIOCHEMICAL FRUIT QUALITY CHARACTERIZATION

Revista Brasileira de Fruticultura ◽

10.1590/0100-29452017669 ◽

2017 ◽

Vol 39 (4) ◽

Author(s):

KELI CRISTINA FABIANE ◽

AMÉRICO WAGNER JÚNIOR ◽

JULIANO ZANELA ◽

CRISTIANO HOSSEL ◽

IDEMIR CITADIN

Keyword(s):

Functional Foods ◽

Phenylalanine Ammonia Lyase ◽

Reducing Sugars ◽

Prunus Persica ◽

Biochemical Characterization ◽

Total Proteins ◽

Breeding Programs ◽

Organoleptic Characteristics ◽

Selection Of

ABSTRACT Peach is much appreciated by consumers and its popularity is mainly related with organoleptic characteristics. However, with emergence of concepts of functional foods (health promoters), there is high interest to study and to quantify the biochemical components of fruits. The aim of this work was to perform the biochemical characterization of peach genotypes, evaluating the genetic diversity and selecting those with desirable biochemical qualities for use as parents in future breeding programs. The experiment was carried out at the Laboratory of Plant Physiology - UTFPR - Campus of Dois Vizinhos, PR (Brazil), with fruits from 26 and 29 peach genotypes (Prunus persica) in the 2009/2010 and 2010/2011 crop years, respectively. The experimental design was entirely randomized, considering each genotype as treatment, using four replicates and four fruits per plot. Total and reducing sugars, total proteins, amino acids, total phenols, anthocyanins, flavonoids and phenylalanine ammonia-lyase enzyme activity (PAL) in fruits were evaluated. According to the results of two crop years, ‘Cascata 967’, ‘Conserva 985’, ‘Kampai’, ‘Tropic Snow’ and ‘Cascata 1055’ were selected as those with the highest levels of these compounds.

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Characterization of the Common Japonica-Originated Genomic Regions in the High-Yielding Varieties Developed from Inter-Subspecific Crosses in Temperate Rice (Oryza sativa L.)

Genes ◽

10.3390/genes11050562 ◽

2020 ◽

Vol 11 (5) ◽

pp. 562 ◽

Cited By ~ 1

Author(s):

Jeonghwan Seo ◽

So-Myeong Lee ◽

Jae-Hyuk Han ◽

Na-Hyun Shin ◽

Yoon Kyung Lee ◽

...

Keyword(s):

Oryza Sativa L ◽

Snp Markers ◽

Yield Potential ◽

Breeding Programs ◽

Wx Gene ◽

High Yielding Varieties ◽

Indica And Japonica Subspecies ◽

Genomic Regions ◽

Next Generation Sequencing Ngs

The inter-subspecific crossing between indica and japonica subspecies in rice have been utilized to improve the yield potential of temperate rice. In this study, a comparative study of the genomic regions in the eight high-yielding varieties (HYVs) was conducted with those of the four non-HYVs. The Next-Generation Sequencing (NGS) mapping on the Nipponbare reference genome identified a total of 14 common genomic regions of japonica-originated alleles. Interestingly, the HYVs shared japonica-originated genomic regions on nine chromosomes, although they were developed through different breeding programs. A panel of 94 varieties was classified into four varietal groups with 38 single nucleotide polymorphism (SNP) markers from 38 genes residing in the japonica-originated genomic regions and 16 additional trait-specific SNPs. As expected, the japonica-originated genomic regions were only present in the japonica (JAP) and HYV groups, except for Chr4-1 and Chr4-2. The Wx gene, located within Chr6-1, was present in the HYV and JAP variety groups, while the yield-related genes were conserved as indica alleles in HYVs. The japonica-originated genomic regions and alleles shared by HYVs can be employed in molecular breeding programs to further develop the HYVs in temperate rice.

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Mapping QTL for spike fertility and related traits in two doubled haploid wheat (Triticum aestivum L.) populations

BMC Plant Biology ◽

10.1186/s12870-021-03061-y ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Nicole Pretini ◽

Leonardo S. Vanzetti ◽

Ignacio I. Terrile ◽

Guillermo Donaire ◽

Fernanda G. González

Keyword(s):

Doubled Haploid ◽

Marker Assisted Selection ◽

Triticum Aestivum L ◽

Physiological Model ◽

Yield Potential ◽

Breeding Programs ◽

Per Se ◽

Genomic Regions ◽

Fertility Traits ◽

Selection Of

Abstract Background In breeding programs, the selection of cultivars with the highest yield potential consisted in the selection of the yield per se, which resulted in cultivars with higher grains per spike (GN) and occasionally increased grain weight (GW) (main numerical components of the yield). In this study, quantitative trait loci (QTL) for GW, GN and spike fertility traits related to GN determination were mapped using two doubled haploid (DH) populations (Baguette Premium 11 × BioINTA 2002 and Baguette 19 × BioINTA 2002). Results In total 305 QTL were identified for 14 traits, out of which 12 QTL were identified in more than three environments and explained more than 10% of the phenotypic variation in at least one environment. Eight hotspot regions were detected on chromosomes 1A, 2B, 3A, 5A, 5B, 7A and 7B in which at least two major and stable QTL sheared confidence intervals. QTL on two of these regions (R5A.1 and R5A.2) have previously been described, but the other six regions are novel. Conclusions Based on the pleiotropic analysis within a robust physiological model we conclude that two hotspot genomic regions (R5A.1 and R5A.2) together with the QGW.perg-6B are of high relevance to be used in marker assisted selection in order to improve the spike yield potential. All the QTL identified for the spike related traits are the first step to search for their candidate genes, which will allow their better manipulation in the future.

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Chromosomal Map of the Model LegumeLotus japonicus

Genetics ◽

10.1093/genetics/161.4.1661 ◽

2002 ◽

Vol 161 (4) ◽

pp. 1661-1672 ◽

Cited By ~ 7

Author(s):

Andrea Pedrosa ◽

Niels Sandal ◽

Jens Stougaard ◽

Dieter Schweizer ◽

Andreas Bachmair

Keyword(s):

Repetitive Sequences ◽

Lotus Japonicus ◽

Chromosome Complement ◽

Linkage Groups ◽

Closely Related Species ◽

F1 Hybrid ◽

Bac Clones ◽

Genomic Regions ◽

Chromosomal Map

AbstractLotus japonicus is a model plant for the legume family. To facilitate map-based cloning approaches and genome analysis, we performed an extensive characterization of the chromosome complement of the species. A detailed karyotype of L. japonicus Gifu was built and plasmid and BAC clones, corresponding to genetically mapped markers (see the accompanying article by Sandal et al. 2002, this issue), were used for FISH to correlate genetic and chromosomal maps. Hybridization of DNA clones from 32 different genomic regions enabled the assignment of linkage groups to chromosomes, the comparison between genetic and physical distances throughout the genome, and the partial characterization of different repetitive sequences, including telomeric and centromeric repeats. Additional analysis of L. filicaulis and its F1 hybrid with L. japonicus demonstrated the occurrence of inversions between these closely related species, suggesting that these chromosome rearrangements are early events in speciation of this group.

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QTL Mapping of Seedling and Adult Plant Resistance to Septoria Tritici Blotch in Winter Wheat cv. Mandub (Triticum aestivum L.)

Agronomy ◽

10.3390/agronomy11061108 ◽

2021 ◽

Vol 11 (6) ◽

pp. 1108

Author(s):

Dominika Piaskowska ◽

Urszula Piechota ◽

Magdalena Radecka-Janusik ◽

Paweł Czembor

Keyword(s):

Mapping Population ◽

Triticum Aestivum L ◽

Seedling Stage ◽

Septoria Tritici Blotch ◽

Septoria Tritici ◽

Adult Plant ◽

Resistance Locus ◽

Phenotypic Variance ◽

Breeding Programs ◽

Plant Stage

Septoria tritici blotch (STB) is one of the most devastating foliar diseases of wheat worldwide. Host resistance is the most economical and safest method of controlling the disease, and information on resistance loci is crucial for effective breeding for resistance programs. In this study we used a mapping population consisting of 126 doubled-haploid lines developed from a cross between the resistant cultivar Mandub and the susceptible cultivar Begra. Three monopycnidiospore isolates of Z. tritici with diverse pathogenicity were used to test the mapping population and parents’ STB resistance at the seedling stage (under a controlled environment) and adult plant stage (polytunnel). For both types of environments, the percentage leaf area covered by necrosis (NEC) and pycnidia (PYC) was determined. A linkage map comprising 5899 DArTSNP and silicoDArT markers was used for the quantitative trait loci (QTL) analysis. The analysis showed five resistance loci on chromosomes 1B, 2B and 5B, four of which were derived from cv. Mandub. The location of QTL detected in our study on chromosomes 1B and 5B may suggest a possible identity or close linkage with Stb2/Stb11/StbWW and Stb1 loci, respectively. QStb.ihar-2B.4 and QStb.ihar-2B.5 detected on chromosome 2B do not co-localize with any known Stb genes. QStb.ihar-2B.4 seems to be a new resistance locus with a moderate effect (explaining 29.3% of NEC and 31.4% of PYC), conferring resistance at the seedling stage. The phenotypic variance explained by QTL detected in cv. Mandub ranged from 11.9% to 70.0%, thus proving that it is a good STB resistance source and can potentially be utilized in breeding programs.

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A New Breeding Strategy towards Introgression and Characterization of Stay-Green QTL for Drought Tolerance in Sorghum

Agriculture ◽

10.3390/agriculture11070598 ◽

2021 ◽

Vol 11 (7) ◽

pp. 598

Author(s):

Nasrein Mohamed Kamal ◽

Yasir Serag Alnor Gorafi ◽

Hanan Abdeltwab ◽

Ishtiag Abdalla ◽

Hisashi Tsujimoto ◽

...

Keyword(s):

Phenotypic Expression ◽

Phenotypic Selection ◽

Breeding Strategy ◽

Stay Green ◽

Breeding Programs ◽

The Public ◽

Drought Tolerant ◽

Selection Step ◽

The Cost

Several marker-assisted selection (MAS) or backcrossing (MAB) approaches exist for polygenic trait improvement. However, the implementation of MAB remains a challenge in many breeding programs, especially in the public sector. In MAB introgression programs, which usually do not include phenotypic selection, undesired donor traits may unexpectedly turn up regardless of how expensive and theoretically powerful a backcross scheme may be. Therefore, combining genotyping and phenotyping during selection will improve understanding of QTL interactions with the environment, especially for minor alleles that maximize the phenotypic expression of the traits. Here, we describe the introgression of stay-green QTL (Stg1–Stg4) from B35 into two sorghum backgrounds through an MAB that combines genotypic and phenotypic (C-MAB) selection during early backcross cycles. The background selection step is excluded. Since it is necessary to decrease further the cost associated with molecular marker assays, the costs of C-MAB were estimated. Lines with stay-green trait and good performance were identified at an early backcross generation, backcross two (BC2). Developed BC2F4 lines were evaluated under irrigated and drought as well as three rainfed environments varied in drought timing and severity. Under drought conditions, the mean grain yield of the most C-MAB-introgression lines was consistently higher than that of the recurrent parents. This study is one of the real applications of the successful use of C-MAB for the development of drought-tolerant sorghum lines for drought-prone areas.

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Genetic diversity of table grape based on morphoagronomic traits

Scientia Agricola ◽

10.1590/s0103-90162011000100007 ◽

2011 ◽

Vol 68 (1) ◽

pp. 42-49 ◽

Cited By ~ 14

Author(s):

Patrícia Coelho de Souza Leão ◽

Cosme Damião Cruz ◽

Sérgio Yoshimitsu Motoike

Keyword(s):

Genetic Diversity ◽

Clustering Analysis ◽

Germplasm Collection ◽

Table Grape ◽

Cluster Method ◽

Breeding Programs ◽

Method Analysis ◽

Vitis Spp ◽

Grape Cultivars

The conservation and characterization of grape (Vitis spp) genetic resources in germplasm banks have been the basis of its use in breeding programs that result in development of new cultivars. There are at least 10,000 grape cultivars kept in germplasm collection. The genetic diversity in 136 table grape accessions from the state of Bahia, Brazil, was evaluated. Continuous and discrete morphoagronomic traits were assessed. The clustering analysis by the Tocher otimization method resulted in 30 clusters (considering continuous morphoagronomic traits), and 9 clusters (taking into consideration multicategorical traits). There was no agreement between clusters obtained by both, continuous or discrete phenotypic descriptors, independent of the cluster method analysis used. A satisfactory genetic variability among the table grape accessions was observed.

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Varietal and Geographical Origin Characterization of Peaches and Nectarines by Combining Analytical Techniques and Statistical Approach

Molecules ◽

10.3390/molecules26144128 ◽

2021 ◽

Vol 26 (14) ◽

pp. 4128

Author(s):

Gabriella Tamasi ◽

Claudia Bonechi ◽

Gemma Leone ◽

Marco Andreassi ◽

Marco Consumi ◽

...

Keyword(s):

Prunus Persica ◽

Antioxidant Properties ◽

Analytical Techniques ◽

Mediterranean Area ◽

Analysis Methodology ◽

Chemometric Approach ◽

Sims Analysis ◽

The Comparative Study ◽

Geographical Characteristics

Prunus persica L. is one of the most important fruit crops in European production, after grapes, apples, oranges and watermelons. Most varieties are rich in secondary metabolites, showing antioxidant properties for human health. The purpose of this study was to develop a chemical analysis methodology, which involves the use of different analytical-instrumental techniques to deepen the knowledge related to the profile of metabolites present in selected cultivars of peaches and nectarines cultivated in the Mediterranean area (Southern Italy). The comparative study was conducted by choosing yellow-fleshed peaches (RomeStar, ZeeLady) and yellow-fleshed nectarines (Nectaross, Venus) from two geographical areas (Piana di Sibari and Piana di Metaponto), and by determining the chemical parameters for the flesh and skin that allow for identification of any distinctive varietal and/or geographical characteristics. A combined analytical and chemometric approach was used, trough rheological, thermogravimetric (TGA), chromatographic (HPLC-ESI-MS), spectroscopic (UV-Vis, ATR-FTIR, NMR) and spectrometric (ToF-SIMS) analysis. This approach allowed us to identify the characterizing parameters for the analysis of a plant matrix so that the developed methodology could define an easily exportable and extendable model for the characterization of other types of vegetable matrices.

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