1
|
Aalborg T, Sverrisdóttir E, Kristensen HT, Nielsen KL. The effect of marker types and density on genomic prediction and GWAS of key performance traits in tetraploid potato. FRONTIERS IN PLANT SCIENCE 2024; 15:1340189. [PMID: 38525152 PMCID: PMC10957621 DOI: 10.3389/fpls.2024.1340189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 02/14/2024] [Indexed: 03/26/2024]
Abstract
Genomic prediction and genome-wide association studies are becoming widely employed in potato key performance trait QTL identifications and to support potato breeding using genomic selection. Elite cultivars are tetraploid and highly heterozygous but also share many common ancestors and generation-spanning inbreeding events, resulting from the clonal propagation of potatoes through seed potatoes. Consequentially, many SNP markers are not in a 1:1 relationship with a single allele variant but shared over several alleles that might exert varying effects on a given trait. The impact of such redundant "diluted" predictors on the statistical models underpinning genome-wide association studies (GWAS) and genomic prediction has scarcely been evaluated despite the potential impact on model accuracy and performance. We evaluated the impact of marker location, marker type, and marker density on the genomic prediction and GWAS of five key performance traits in tetraploid potato (chipping quality, dry matter content, length/width ratio, senescence, and yield). A 762-offspring panel of a diallel cross of 18 elite cultivars was genotyped by sequencing, and markers were annotated according to a reference genome. Genomic prediction models (GBLUP) were trained on four marker subsets [non-synonymous (29,553 SNPs), synonymous (31,229), non-coding (32,388), and a combination], and robustness to marker reduction was investigated. Single-marker regression GWAS was performed for each trait and marker subset. The best cross-validated prediction correlation coefficients of 0.54, 0.75, 0.49, 0.35, and 0.28 were obtained for chipping quality, dry matter content, length/width ratio, senescence, and yield, respectively. The trait prediction abilities were similar across all marker types, with only non-synonymous variants improving yield predictive ability by 16%. Marker reduction response did not depend on marker type but rather on trait. Traits with high predictive abilities, e.g., dry matter content, reached a plateau using fewer markers than traits with intermediate-low correlations, such as yield. The predictions were unbiased across all traits, marker types, and all marker densities >100 SNPs. Our results suggest that using non-synonymous variants does not enhance the performance of genomic prediction of most traits. The major known QTLs were identified by GWAS and were reproducible across exonic and whole-genome variant sets for dry matter content, length/width ratio, and senescence. In contrast, minor QTL detection was marker type dependent.
Collapse
Affiliation(s)
- Trine Aalborg
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | | | | | | |
Collapse
|
2
|
Li J, Cullis C. Comparative Analysis of Tylosema esculentum Mitochondrial DNA Revealed Two Distinct Genome Structures. BIOLOGY 2023; 12:1244. [PMID: 37759643 PMCID: PMC10525999 DOI: 10.3390/biology12091244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 09/11/2023] [Accepted: 09/13/2023] [Indexed: 09/29/2023]
Abstract
Tylosema esculentum, commonly known as the marama bean, is an underutilized legume with nutritious seeds, holding potential to enhance food security in southern Africa due to its resilience to prolonged drought and heat. To promote the selection of this agronomically valuable germplasm, this study assembled and compared the mitogenomes of 84 marama individuals, identifying variations in genome structure, single-nucleotide polymorphisms (SNPs), insertions/deletions (indels), heteroplasmy, and horizontal transfer. Two distinct germplasms were identified, and a novel mitogenome structure consisting of three circular molecules and one long linear chromosome was discovered. The structural variation led to an increased copy number of specific genes, nad5, nad9, rrnS, rrn5, trnC, and trnfM. The two mitogenomes also exhibited differences at 230 loci, with only one notable nonsynonymous substitution in the matR gene. Heteroplasmy was concentrated at certain loci on chromosome LS1 (OK638188). Moreover, the marama mitogenome contained an over 9 kb insertion of cpDNA, originating from chloroplast genomes, but had accumulated mutations and lost gene functionality. The evolutionary and comparative genomics analysis indicated that mitogenome divergence in marama might not be solely constrained by geographical factors. Additionally, marama, as a member from the Cercidoideae subfamily, tends to possess a more complete set of mitochondrial genes than Faboideae legumes.
Collapse
Affiliation(s)
| | - Christopher Cullis
- Department of Biology, Case Western Reserve University, Cleveland, OH 44106, USA;
| |
Collapse
|
3
|
Voronkova EV, Luksha VI, Poliukhovich JV, Gukasian ON, Zharich VM, Yermishin AP. Male fertility of varieties of potato whith different cytoplasma type. DOKLADY OF THE NATIONAL ACADEMY OF SCIENCES OF BELARUS 2023. [DOI: 10.29235/1561-8323-2023-67-1-41-50] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/10/2023]
Abstract
The predominance of varieties and parental lines having low male fertility is a characteristic feature of potatoes as a culture with asexual reproduction. The growth of the share of male sterile varieties has been recently noticed as a result of use in breeding interspecific hybrids with sterile-type cytoplasm. It leads to narrowing the genetic basis of modern potato varieties since it limits the choice of pollinators for breeding. The objectives of this research were to assess male fertility characters of 130 potato varieties from the collection of the Institute of Genetics and Cytology of the National Academy of Sciences of Belarus and identify their cytoplasm type using the set of DNA markers. The obtained results are intended for selection of pollinators for conventional breeding of potato, as well as of varieties for production of dihaploids with fertile-type cytoplasm suitable for hybrid breeding at the diploid level. It was revealed that the accessions with T- and D-type cytoplasm prevailed in the collection (46.0 and 35.4 %, respectively), the share of the accessions with W-type cytoplasm was 18.5 %. Most of the effective pollinators were selected among the varieties having T/β-type cytoplasm (44.6 %). The varieties Aksamit, Briz, Dubrava, Uladar, Alwara, Ausonia, Carlita, Fresco, Labadia, Latona, Liu, Lyra, Quarta, Satina, Sissi with this cytoplasm type were selected as most promising for our purposes according to the combination of breeding characters. The potato varieties with D/α-type cytoplasm were present in the collection under study. Approximately one third (32.6 %) was able to produce functionally fertile pollen (PFF), however the level of its fertility was as a rule low. Nevertheless, the varieties Bashkirski, Delfin, Olga and Ponto formed pollen with PFF suitable to guarantee seed production in crosses. Most of the studied varieties with W/α-, W/β-, and W/γ-type cytoplasm were male sterile. The varieties Atlant and Vesna Belaya were revealed among them that were able to produce functionally fertile pollen.
Collapse
Affiliation(s)
- E. V. Voronkova
- Institute of Genetics and Cytology of the National Academy of Science of Belarus
| | - V. I. Luksha
- Institute of Genetics and Cytology of the National Academy of Science of Belarus
| | - J. V. Poliukhovich
- Institute of Genetics and Cytology of the National Academy of Science of Belarus
| | - O. N. Gukasian
- Institute of Genetics and Cytology of the National Academy of Science of Belarus
| | - V. M. Zharich
- Institute of Genetics and Cytology of the National Academy of Science of Belarus
| | - A. P. Yermishin
- Institute of Genetics and Cytology of the National Academy of Science of Belarus
| |
Collapse
|
4
|
Gavrilenko T, Chukhina I, Antonova O, Krylova E, Shipilina L, Oskina N, Kostina L. Comparative Analysis of the Genetic Diversity of Chilean Cultivated Potato Based on a Molecular Study of Authentic Herbarium Specimens and Present-Day Gene Bank Accessions. PLANTS (BASEL, SWITZERLAND) 2022; 12:174. [PMID: 36616303 PMCID: PMC9823414 DOI: 10.3390/plants12010174] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Revised: 12/19/2022] [Accepted: 12/28/2022] [Indexed: 06/17/2023]
Abstract
At the end of the 1920s, Vavilov organized several potato-collecting missions in South and Central America. Vavilov and his colleagues, Juzepczuk and Bukasov, participated in these expeditions and worked on gathered material, designated two centers of potato varietal riches and diversity-the Peru-Bolivia high-mountain center and the southern coast of Chile. The WIR Herbarium holds authentic specimens of many taxa described by Russian taxonomists. Here, a set of 20 plastid DNA-specific markers was applied for 49 authentic herbarium specimens of Solanum tuberosum L. from the WIR Herbarium to analyze the genetic diversity of the landrace population collected by Juzepczuk in 1928 in southern-central Chile. Two plastid DNA types, T and A, and two chlorotypes were identified in herbarium specimens, with a clear predominance (96%) of chlorotype cpT_III. In addition, we analyzed 46 living Chilean accessions from the VIR field potato gene bank that were collected after the appearance of Phytophthora infestans in Chile. These living accessions were differentiated into four chlorotypes. Finding a D-type cytoplasm in living Chilean accessions that possess two new chlorotypes indicates a replacement of native cultivars and introgression from the wild Mexican species S. demissum that was actively used in breeding as a source of race-specific resistance to late blight.
Collapse
|
5
|
Sanetomo R, Akai K, Nashiki A. Discovery of a novel mitochondrial DNA molecule associated with tetrad pollen sterility in potato. BMC PLANT BIOLOGY 2022; 22:302. [PMID: 35725378 PMCID: PMC9210639 DOI: 10.1186/s12870-022-03669-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Accepted: 05/31/2022] [Indexed: 06/01/2023]
Abstract
BACKGROUND Tetrad sterility in potato is caused by a specific cytoplasm, called TSCsto, derived from the Mexican wild tetraploid species Solanum stoloniferum. Different S. stoloniferum accessions crossed as females with S. tuberosum resulted in 12 fertile hybrids and 27 sterile hybrids exhibiting tetrad sterility. RESULTS Whole-mitochondrial-genome sequencing was performed for two fertile hybrids and three hybrids exhibiting tetrad sterility. Two to seven contigs, with the total assembly lengths ranging from 462,716 to 535,375 bp, were assembled for each hybrid. Unlike for the reference mitochondrial genome (cv. Désirée), two different recombinant-type contigs (RC-I and RC-II) were identified. RC-I featured by the rpl5-ψrps14 gene joined to the nad6 gene, generating a novel intergenic region. Using a PCR marker (P-3), we found that this intergenic region occurred exclusively in interspecific hybrids exhibiting tetrad sterility and in their parental S. stoloniferum accessions. A part of this intergenic sequence was expressed in the pollen. From a large survey in which P-3 was applied to 129 accessions of 27 mostly Mexican wild species, RC-I was found in diploid S. verrucosum and polyploid species. From eight accessions of S. verrucosum used as females, 92 interspecific hybrids were generated, in which only those carrying RC-I exhibited tetrad sterility. CONCLUSIONS RC-I was clearly associated with tetrad sterility, and the RC-I-specific intergenic region likely contains a causal factor of tetrad sterility.
Collapse
Affiliation(s)
- Rena Sanetomo
- Potato Germplasm Enhancement Laboratory, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Hokkaido, 080-8555, Japan.
| | - Kotaro Akai
- National Agriculture and Food Research Organization, Hokkaido Agricultural Research Center, Memuro, Hokkaido, 082-0081, Japan
| | - Akito Nashiki
- Potato Germplasm Enhancement Laboratory, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Hokkaido, 080-8555, Japan
- Graduate School of Science and Technology, The University of Tsukuba, Tsukuba, Ibaraki, 305-8572, Japan
| |
Collapse
|
6
|
Genetic Diversity Trends in the Cultivated Potato: A Spatiotemporal Overview. BIOLOGY 2022; 11:biology11040604. [PMID: 35453803 PMCID: PMC9026384 DOI: 10.3390/biology11040604] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 04/01/2022] [Accepted: 04/14/2022] [Indexed: 11/27/2022]
Abstract
Simple Summary Monitoring the change in genetic diversity over time and space in crop species is essential to facilitating further improvement. As the world’s most important tuber crop for human consumption, and an ideal candidate to help address global food security, the cultivated potato deserves in-depth study in this regard. In this overview, some aspects of spatiotemporal diversity assessment in the cultivated potato are examined with the aim of promoting appropriate strategies for breeding programs in line with challenges relating to sustainable crop production. Abstract We investigated the changes in genetic diversity over time and space of the cultivated potato (Solanum tuberosum L.) for the period pre-1800 to 2021. A substantial panel of 1219 potato varieties, belonging to different spatiotemporal groups, was examined using a set of 35 microsatellite markers (SSR). Genotypic data covering a total of 407 alleles was analyzed using both self-organizing map (SOM) and discriminant analysis of principal components (DAPC) de novo and a priori clustering methods, respectively. Data analysis based on different models of genetic structuring provided evidence of (1) at least two early lineages that have been maintained since their initial introduction from the Andes into Europe in the 16th century, followed by later ones coming from reintroduction events from the US in the mid-1800s; (2) a level of diversity that has gradually evolved throughout the studied time periods and areas, with the most modern variety groups encompassing most of the diversity found in earlier decades; (3) the emergence of new genetic groups within the current population due to increases in the use of germplasm enhancement practices using exotic germplasms. In addition, analysis revealed significant genetic differentiation both among and within the spatiotemporal groups of germplasm studied. Our results therefore highlight that no major genetic narrowing events have occurred within the cultivated potato over the past three centuries. On the contrary, the genetic base shows promising signs of improvement, thanks to extensive breeding work that is gaining momentum. This overview could be drawn on not only to understand better how past decisions have impacted the current genetic cultivated potato resources, but also to develop appropriate new strategies for breeding programs consistent with the socio-economic and sustainability challenges faced by agrifood systems.
Collapse
|
7
|
Szajko K, Sołtys-Kalina D, Heidorn-Czarna M, Smyda-Dajmund P, Wasilewicz-Flis I, Jańska H, Marczewski W. Transcriptomic and proteomic data provide new insights into cold-treated potato tubers with T- and D-type cytoplasm. PLANTA 2022; 255:97. [PMID: 35380306 PMCID: PMC8983635 DOI: 10.1007/s00425-022-03879-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 03/17/2022] [Indexed: 06/14/2023]
Abstract
Tuber-omics in potato with the T- and D-types of cytoplasm showed different sets of differentially expressed genes and proteins in response to cold storage. For the first time, we report differences in gene and protein expression in potato (Solanum tuberosum L.) tubers possessing the T- or D-type cytoplasm. Two F1 diploid reciprocal populations, referred to as T and D, were used. The pooling strategy was applied for detection of differentially expressed genes (DEGs) and differentially expressed proteins (DEPs) in tubers consisting of extreme chip colour after cold storage. RNA and protein bulks were constructed from contrasting phenotypes. We recognized 48 and 15 DEGs for the T and D progenies, respectively. DEPs were identified in the amyloplast and mitochondrial fractions. In the T-type cytoplasm, only 2 amyloplast-associated and 5 mitochondria-associated DEPs were detected. Of 37 mitochondria-associated DEPs in the D-type cytoplasm, there were 36 downregulated DEPs in the dark chip colour bulks. These findings suggest that T- and D-type of cytoplasm might influence sugar accumulation in cold-stored potato tubers in different ways. We showed that the mt/nucDNA ratio was higher in D-possessing tubers after cold storage than in T progeny. For the D-type cytoplasm, the pt/nucDNA ratio was higher for tubers characterized by dark chip colour than for those with light chip colour. Our findings suggest that T- and D-type cytoplasm might influence sugar accumulation in cold-stored potato tubers in different ways.
Collapse
Affiliation(s)
- Katarzyna Szajko
- Plant Breeding and Acclimatization Institute-National Research Institute, Platanowa 19, 05-831, Młochów, Poland.
| | - Dorota Sołtys-Kalina
- Plant Breeding and Acclimatization Institute-National Research Institute, Platanowa 19, 05-831, Młochów, Poland
| | | | - Paulina Smyda-Dajmund
- Plant Breeding and Acclimatization Institute-National Research Institute, Platanowa 19, 05-831, Młochów, Poland
| | - Iwona Wasilewicz-Flis
- Plant Breeding and Acclimatization Institute-National Research Institute, Platanowa 19, 05-831, Młochów, Poland
| | - Hanna Jańska
- Faculty of Biotechnology, University of Wroclaw, 50-383, Wrocław, Poland
| | - Waldemar Marczewski
- Plant Breeding and Acclimatization Institute-National Research Institute, Platanowa 19, 05-831, Młochów, Poland.
| |
Collapse
|
8
|
Achakkagari SR, Tai HH, Davidson C, De Jong H, Strömvik MV. The complete mitogenome assemblies of ten diploid potato clones reveal recombination and overlapping variants. DNA Res 2021; 28:6319723. [PMID: 34254134 PMCID: PMC8386665 DOI: 10.1093/dnares/dsab009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 07/07/2021] [Indexed: 01/30/2023] Open
Abstract
The potato mitogenome is complex and to understand various biological functions and nuclear-cytoplasmic interactions, it is important to characterize its gene content and structure. In this study, the complete mitogenome sequences of nine diploid potato clones along with a diploid Solanum okadae clone were characterized. Each mitogenome was assembled and annotated from Pacific Biosciences (PacBio) long-reads and 10X genomics short reads. The results show that each mitogenome consists of multiple circular molecules with similar structure and gene organization, though two groups (clones 07506-01, DW84-1457, 08675-21, and H412-1 in one group, and clones W5281-2, 12625-02, 12120-03, and 11379-03 in another group) could be distinguished, and two mitogenomes (clone 10908-06 and OKA15) were not consistent with those or with each other. Significant differences in the repeat structure of the ten mitogenomes were found, as was recombination events leading to multiple sub-genomic circles. Comparison between individual molecules revealed a translocation of ∼774 bp region located between a short repeat of 40 bp in molecule 3 of each mitogenome, and an insertion of the same in the molecule 2 of the 10908-06 mitogenome. Finally, phylogenetic analyses revealed a close relationship between the mitogenomes of these clones and previously published potato mitogenomes.
Collapse
Affiliation(s)
| | - Helen H Tai
- Fredericton Research and Development Centre, Agriculture and Agri-Food Canada, Fredericton, Canada
| | - Charlotte Davidson
- Fredericton Research and Development Centre, Agriculture and Agri-Food Canada, Fredericton, Canada
| | - Hielke De Jong
- Fredericton Research and Development Centre, Agriculture and Agri-Food Canada, Fredericton, Canada
| | | |
Collapse
|
9
|
Park TH. Complete chloroplast genome sequence of the wild diploid potato relative, Solanum acaule. Mitochondrial DNA B Resour 2021; 6:1189-1191. [PMID: 33829083 PMCID: PMC8008929 DOI: 10.1080/23802359.2021.1902414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/29/2022] Open
Affiliation(s)
- Tae-Ho Park
- Department of Horticulture, Daegu University, Gyeongsan, South Korea
| |
Collapse
|
10
|
Sood S, Kumar A, Singh B, S S, Bhardwaj V. Cytoplasmic genome of Indian potato varieties and breeding lines vis a vis prospects in potato breeding. Heliyon 2021; 7:e06365. [PMID: 33732923 PMCID: PMC7937657 DOI: 10.1016/j.heliyon.2021.e06365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Revised: 05/25/2020] [Accepted: 02/22/2021] [Indexed: 11/19/2022] Open
Abstract
Advances in research resulted in development of a simple, rapid and reliable multiplex PCR protocol for cytoplasm differentiation in potato. Applying this rapid technique, we assessed the cytoplasm diversity in 57 Indian potato varieties, 15 popular exotic varieties and 47 biotic stress resistance breeding parental lines using five DNA based markers. Results revealed that T is the predominant cytoplasm type followed by D in Indian and exotic potato varieties as well as parental lines. The proportion of T and D type cytoplasm was 77.2% and 19.3% and 73.3% and 20.0% in Indian and exotic varieties, respectively. A and W type were found in one variety each, while M and P were missing in Indian varieties. All the popular Indian table potato varieties have tuberosum type cytoplasm with few exceptions of varieties bred for biotic stress resistance namely Kufri Himalini, Kufri Girdhari, carrying demissum cytoplasm. Opposite was true for Indian processing cultivars with the exception of Kufri Chipsona 4, which had T type cytoplasm. Evaluation of biotic stress resistance breeding parental lines showed increasing use of D (34.0%) and W (12.8%) cytoplasm in comparison to previously bred varieties. Although D type cytoplasm is associated with late blight resistance and male sterility, all Indian cultivars with D type cytoplasm are not resistant to late blight, nor they all are male sterile. Male fertile D type cytoplasm and the cytoplasms showing good interaction between cytoplasmic and nuclear gene for agronomic traits should be incorporated in the parental lines. Efforts must also be done to diversify the cytoplasm of cultivated potato with at least semi-cultivated cytoplasm types.
Collapse
|
11
|
Anisimova IN. Structural and Functional Organization of Genes That Induce and Suppress Cytoplasmic Male Sterility in Plants. RUSS J GENET+ 2020. [DOI: 10.1134/s1022795420110022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
12
|
Achakkagari SR, Kyriakidou M, Tai HH, Anglin NL, Ellis D, Strömvik MV. Complete plastome assemblies from a panel of 13 diverse potato taxa. PLoS One 2020; 15:e0240124. [PMID: 33031462 PMCID: PMC7544113 DOI: 10.1371/journal.pone.0240124] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 09/20/2020] [Indexed: 01/24/2023] Open
Abstract
The chloroplasts are a crucial part of photosynthesizing plant cells and are extensively utilized in phylogenetic studies mainly due to their maternal inheritance. Characterization and analysis of complete plastome sequences is necessary to understand their diversity and evolutionary relationships. Here, a panel of thirteen plastomes from various potato taxa are presented. Though they are highly similar with respect to gene order and content, there is also a great extent of SNPs and InDels between them, with one of the Solanum bukasovii plastomes (BUK2) having the highest number of SNPs and InDels. Five different potato plastome types (C, S, A, W, W2) are present in the panel. Interestingly, the S. tuberosum subsp. tuberosum (TBR) accession has a W-type plastome, which is not commonly found in this species. The S-type plastome has a conserved 48 bp deletion not found in other types, which is responsible for the divergence of the S-type from the C-type plastome. Finally, a phylogenetic analysis shows that these plastomes cluster according to their types. Congruence between the nuclear genome and the plastome phylogeny of these accessions was seen, however with considerable differences, supporting the hypothesis of introgression and hybridization between potato species.
Collapse
Affiliation(s)
| | - Maria Kyriakidou
- Department of Plant Science, McGill University, Montreal, Canada
| | - Helen H. Tai
- Fredericton Research and Development Centre, Agriculture and Agri-Food Canada, Fredericton, Canada
| | | | | | | |
Collapse
|
13
|
Smyda-Dajmund P, Śliwka J, Janiszewska M, Zimnoch-Guzowska E. Cytoplasmic diversity of potato relatives preserved at Plant Breeding and Acclimatization Institute in Poland. Mol Biol Rep 2020; 47:3929-3935. [PMID: 32406017 PMCID: PMC7239805 DOI: 10.1007/s11033-020-05486-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 04/30/2020] [Indexed: 11/06/2022]
Abstract
Among different types of potato cytoplasmic genomes, some are associated with male sterility or affect agronomic traits. The goal of this study was to analyze types of chloroplast and mitochondrial genomes of selected potato relatives originating from collection of the Institute of Plant Industry, Saint Petersburg, Russia, and preserved in Poland. Using chloroplast and mitochondrial markers the cytoplasm types were determined for 401 genotypes belonging to 43 seed accessions of 28 Solanum species. Among characterized genotypes, 201 (50.1%), 156 (38.9%) and 44 (11%) had cytoplasm types W, D, M, respectively. No accessions with the T, P or A cytoplasm were found. Within cytoplasm W, genotypes with the subtypes: W/α and W/β were identified, but not with W/γ. In S. famatinae, we detected unusual product of the T marker with 65 bp insertion earlier seen exclusively in S. vernei. Among the genotypes of S. leptophyes, two profiles of the ALM_4/ALM_5 marker were observed. S. famatinae and S. vernei come from Argentina, provinces Catamarca and Tucumán. Possibly the insertion in marker T occurred independently in two species, or the accessions were misidentified. Segregation of the ALM_4/ALM_5 marker within S. leptophyes indicates that potato seed accessions are heterogeneous not only due to nuclear DNA polymorphisms but have diversified cytoplasm, too. Our findings are important for exploitation of the tested material in potato breeding. Male-fertile cytoplasm types give a chance of avoiding fertility problems and widening the range of crosses in future generations of breeding materials.
Collapse
Affiliation(s)
- Paulina Smyda-Dajmund
- Plant Breeding and Acclimatization Institute-National Research Institute, Młochów Research Center, Platanowa 19, 05-831, Młochów, Poland.
| | - Jadwiga Śliwka
- Plant Breeding and Acclimatization Institute-National Research Institute, Młochów Research Center, Platanowa 19, 05-831, Młochów, Poland
| | - Marta Janiszewska
- Plant Breeding and Acclimatization Institute-National Research Institute, Młochów Research Center, Platanowa 19, 05-831, Młochów, Poland
| | - Ewa Zimnoch-Guzowska
- Plant Breeding and Acclimatization Institute-National Research Institute, Młochów Research Center, Platanowa 19, 05-831, Młochów, Poland
| |
Collapse
|
14
|
Bdolach E, Prusty MR, Faigenboim-Doron A, Filichkin T, Helgerson L, Schmid KJ, Greiner S, Fridman E. Thermal plasticity of the circadian clock is under nuclear and cytoplasmic control in wild barley. PLANT, CELL & ENVIRONMENT 2019; 42:3105-3120. [PMID: 31272129 DOI: 10.1111/pce.13606] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 06/27/2019] [Accepted: 06/30/2019] [Indexed: 06/09/2023]
Abstract
Temperature compensation, expressed as the ability to maintain clock characteristics (mainly period) in face of temperature changes, that is, robustness, is considered a key feature of circadian clock systems. In this study, we explore the genetic basis for lack of robustness, that is, plasticity, of circadian clock as reflected by photosynthesis rhythmicity. The clock rhythmicity of a new wild barley reciprocal doubled haploid population was analysed with a high temporal resolution of pulsed amplitude modulation of chlorophyll fluorescence under optimal (22°C) and high (32°C) temperature. This comparison between two environments pointed to the prevalence of clock acceleration under heat. Genotyping by sequencing of doubled haploid lines indicated a rich recombination landscape with minor fixation (less than 8%) for one of the parental alleles. Quantitative genetic analysis included genotype by environment interactions and binary-threshold models. Variation in the circadian rhythm plasticity phenotypes, expressed as change (delta) of period and amplitude under two temperatures, was associated with maternal organelle genome (the plasmotype), as well as with several nuclear loci. This first reported rhythmicity driven by nuclear loci and plasmotype with few identified variants, paves the way for studying impact of cytonuclear variations on clock robustness and on plant adaptation to changing environments.
Collapse
Affiliation(s)
- Eyal Bdolach
- Plant Sciences Institute, Volcani Agricultural Research Organization (ARO), Bet Dagan, Israel
- Department of Life Sciences, Ben-Gurion University, Beer-Sheva, Israel
| | - Manas Ranjan Prusty
- Plant Sciences Institute, Volcani Agricultural Research Organization (ARO), Bet Dagan, Israel
| | - Adi Faigenboim-Doron
- Plant Sciences Institute, Volcani Agricultural Research Organization (ARO), Bet Dagan, Israel
| | - Tanya Filichkin
- Crop and Soil Science Department, Oregon State University, Corvallis, Oregon
| | - Laura Helgerson
- Crop and Soil Science Department, Oregon State University, Corvallis, Oregon
| | - Karl J Schmid
- Institute of Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, Stuttgart, Germany
| | - Stephan Greiner
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, Germany
| | - Eyal Fridman
- Plant Sciences Institute, Volcani Agricultural Research Organization (ARO), Bet Dagan, Israel
| |
Collapse
|
15
|
Gavrilenko ТA, Klimenko NS, Alpatieva NV, Kostina LI, Lebedeva VA, Evdokimova ZZ, Apalikova OV, Novikova LY, Antonova OY. Cytoplasmic genetic diversity of potato varieties bred in Russia and FSU countries. Vavilovskii Zhurnal Genet Selektsii 2019. [DOI: 10.18699/vj19.534] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Affiliation(s)
- Т. A. Gavrilenko
- Federal Research Center the N.I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR); St. Petersburg State University
| | - N. S. Klimenko
- Federal Research Center the N.I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR)
| | - N. V. Alpatieva
- Federal Research Center the N.I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR)
| | - L. I. Kostina
- Federal Research Center the N.I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR)
| | - V. A. Lebedeva
- Leningrad Research Institute for Applied Agricultural Science (Belogorka)
| | - Z. Z. Evdokimova
- Leningrad Research Institute for Applied Agricultural Science (Belogorka)
| | - O. V. Apalikova
- Federal Research Center the N.I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR)
| | - L. Y. Novikova
- Federal Research Center the N.I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR)
| | - O. Yu. Antonova
- Federal Research Center the N.I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR)
| |
Collapse
|
16
|
Anisimova IN, Alpatieva NV, Karabitsina YI, Gavrilenko TA. Nucleotide sequence polymorphism in the RFL-PPR genes of potato. J Genet 2019; 98:87. [PMID: 31544787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Cytoplasmic male sterility (CMS) is widely used for hybrid seed production in cultivated Solanaceae species. However, there is very limited information about CMS-Rf genetic systems in potato (Solanum tuberosum). Studying the CMS-Rf systems in potato is both of theoretical and practical significance due to the emergence of a new revolutionary strategy of reinventing potato as adiploid inbred line-based crop to develop F1 hybrid seed potato breeding (Lindhout et al. 2011; Jansky et al. 2016). To search for potato Rf gene candidates, the comparative genetic approach was applied. Based on similarity to petunia Rf-PPR592 gene, 38 fragments were identified in five loci of the whole-genome nucleotide sequence of the accession DM 1-3 516 R44 S. tuberosum Phureja group (https://blast.ncbi.nlm.nih.gov/Blast.cgi). The putative encoded mitochondrial proteins have 589-597 amino acid residues, similarto RF-PPR proteins of petunia and chili pepper and contain 14 or 15 PPR motifs. Primers have been developed flanking the most variable 782-865 bp regions of the selected loci, and polymorphism of the cloned fragments has been investigated in a subset of nine potato genotypes. The amplified fragments included seven or eight PPR motifs and lacked introns. The SNP frequencies ranged from 7.0 to 19.8% depending on the locus, while the ratio of nonsynonymous to synonymous substitutions varied between 0.9 and 2.1. Positions 1, 3 and 6 were the most variable in the studied PPR motifs. Our results demonstrated that the analysed sequences belong to the RFL-PPR gene subfamily and may be considered as Rf gene candidates in potato.
Collapse
Affiliation(s)
- Irina N Anisimova
- Federal Research Centre, The N. I. Vavilov All-Russian Institute of Plant Genetic Resources, Saint Petersburg 190000, Russia.
| | | | | | | |
Collapse
|
17
|
Anisimova IN, Alpatieva NV, Karabitsina YI, Gavrilenko TA. Nucleotide sequence polymorphism in the RFL-PPR genes of potato. J Genet 2019. [DOI: 10.1007/s12041-019-1130-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
|
18
|
Metabolic Alterations in Male-Sterile Potato as Compared to Male-Fertile. Metabolites 2019; 9:metabo9020024. [PMID: 30717245 PMCID: PMC6409681 DOI: 10.3390/metabo9020024] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 01/21/2019] [Accepted: 01/22/2019] [Indexed: 01/22/2023] Open
Abstract
The common potato, Solanum tuberosum L., is the fourth most important agricultural crop worldwide. Until recently, vegetative propagation by tubers has been the main method of potato cultivation. A shift of interest to sexual potato reproduction by true botanical seeds is due to the appearance of a new hybrid seed breeding strategy whose successful application for many crop species has been supported by male sterility. This investigation was focused on the study of differences in the metabolite profiles of anthers at the mature pollen stage from male-fertile and male-sterile genotypes of S. tuberosum. Application of gas chromatography coupled with a mass spectrometry method allowed detection of metabolic profiles for 192 compounds. Further data analysis with several libraries fully identified 75 metabolites; a similar amount was defined up to the classes. Metabolic profiles in the anthers of fertile genotypes were significantly distinguished from male-sterile ones by the accumulation of carbohydrates, while the anthers of sterile genotypes contained a higher amount of amino acids. In comparison with male-fertile plants, male-sterile genotypes had undeveloped pollen grain characters; i.e., smaller grain size, a thicker exine, “permanent tetrads” that failed to disintegrate into microspores, and the absence of pollen apertures that might be due to a disorder in the metabolism of carbohydrates and fatty acids.
Collapse
|
19
|
Characterization for Drought Tolerance and Physiological Efficiency in Novel Cytoplasmic Male Sterile Sources of Sunflower (Helianthus annuus L.). AGRONOMY-BASEL 2018. [DOI: 10.3390/agronomy8100232] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Sunflower is sensitive to drought, and furthermore, sunflower hybrids display limited cytoplasmic diversity. In addition, the wild cytoplasmic sources of sunflower are not well explored for their potential to introduce drought tolerance into newly developed hybrids. Therefore here, we carried out a Line × Tester-based genetic study using 19 sunflower genotypes representing, 13 cytoplasmic male sterile (CMS) lines from wild and conventional sources, 2 maintainer lines, and 4 restorer lines. The CMS and maintainer lines were crossed with restorer lines to develop sixty F1 hybrids. The parents and their hybrids were evaluated under two water regimes, normal irrigation and drought stress (i.e., withholding water). A total of twelve important plant descriptors were studied over a period of two years and the significant differences between parents and hybrids are reported here. More specifically, hybrid lines were higher in average values for all the descriptors. The contribution of female parent was more prominent in the expression of traits in hybrids as compared to male parents. The CMS sources varied significantly regarding seed yield per plant and other physiological traits. Proline content in the leaves of all the genotypes was three times higher in the water stress regime. Accession CMS-PKU-2A was identified as the best general combiner for leaf area and specific leaf weight., whereas CMS-234A was the best general combiner for biological yield and photosynthetic efficiency under both conditions. The cross combinations CMS-ARG-2A × RCR-8297, CMS-234A × P124R, and CMS-38A × P124R were found significant for biological yield, seed yield and oil content under both environments. Overall, this study provides useful information about the cytoplasmic effects on important sunflower traits and drought stress tolerance.
Collapse
|
20
|
Antonova OY, Klimenko NS, Evdokimova ZZ, Kostina LI, Gavrilenko TA. Finding RB/Rpi-blb1/Rpi-sto1-like sequences in conventionally bred potato varieties. Vavilovskii Zhurnal Genet Selektsii 2018. [DOI: 10.18699/vj18.412] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The main objectives in potato breeding are increasing yield abilities and improving resistance to numerous pathogens and pests. Among them, the late blight caused by the Phytophthora infestans oomycete is one of the most destructive potato diseases both in Russia and worldwide. Wild relatives of cultivated potato are traditionally used in breeding as the source of valuable R genes conferring resistance to pathogens. Of particular interest are Mexican wild species because Mexico is the centre of origin and diversity of P. infestans and at the same time, it is the centre of potato species diversity. Mexican wild potato species S. bulbocastanum and S. stoloniferum are an important source of the R genes conferring broad-spec trum resistance against various isolates of P. infestans (Rpi-blb1, Rpi-blb2, Rpi-sto1). Recently these genes have been transferred into cultivated potato gene pool using the cisgene approach. At the same time there is a high probability of finding geno types with the Rpi-sto1 gene (functional homologues of Rpi-blb1) among conventionally bred varieties because for about 40 years S. stoloniferum has been used in breeding as a source of the Rysto and Ry-fsto genes of the extreme resistance to the most important viral pathogen PVY. In this study 188 potato varieties bred in Russia and in near-abroad countries were screened for the presence of six gene-specific markers of the RB/Rpi-blb1 = Rpi-sto1 and Rpi-blb2 genes conferring broad-spectrum resistance against P. infestans, and for the markers linked to the Rysto and Ry-fsto genes conferring extreme resistance to PVY. In addition, a marker for detecting male sterile mitochondrial DNA type gamma derived from S. stoloniferum was used. The genotypes selected through the molecular markers were divided into four groups: (A) 13 PVY resistant varieties carrying diagnostic markers of the Rysto, Ry-fsto genes and having sterile mt-type gamma; (B) four varieties possessing mt-type gamma and not having the markers of the R genes introgressed from S. stoloniferum; (C) eight genotypes carrying five gene-specific markers for the RB/Rpi-blb1/= Rpi-sto1; (D) the rest 166 (86.9 %) varieties not possessing any of the diagnostic markers associated with the S. stoloniferum genetic material. The sequences of the Rpi-sto1- and BLB1 F/R-amplicons were identical in all the genotypes of group ‘C’ and showed respective 99 % and 100 % similarity to the corresponding fragments of the Rpi-sto1 and Rpi-blb1 genes from the GenBank database. Among the genotypes of group ‘C’ various mt-types were detected, and some of them were male fertile.
Collapse
Affiliation(s)
- O. Y. Antonova
- Federal Research Center the N.I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR)
| | - N. S. Klimenko
- Federal Research Center the N.I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR)
| | | | - L. I. Kostina
- Federal Research Center the N.I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR)
| | - T. A. Gavrilenko
- Federal Research Center the N.I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR); St. Petersburg State University, Biological faculty
| |
Collapse
|
21
|
Reddemann A, Horn R. Recombination Events Involving the atp9 Gene Are Associated with Male Sterility of CMS PET2 in Sunflower. Int J Mol Sci 2018; 19:E806. [PMID: 29534485 PMCID: PMC5877667 DOI: 10.3390/ijms19030806] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 03/05/2018] [Accepted: 03/06/2018] [Indexed: 12/18/2022] Open
Abstract
Cytoplasmic male sterility (CMS) systems represent ideal mutants to study the role of mitochondria in pollen development. In sunflower, CMS PET2 also has the potential to become an alternative CMS source for commercial sunflower hybrid breeding. CMS PET2 originates from an interspecific cross of H. petiolaris and H. annuus as CMS PET1, but results in a different CMS mechanism. Southern analyses revealed differences for atp6, atp9 and cob between CMS PET2, CMS PET1 and the male-fertile line HA89. A second identical copy of atp6 was present on an additional CMS PET2-specific fragment. In addition, the atp9 gene was duplicated. However, this duplication was followed by an insertion of 271 bp of unknown origin in the 5' coding region of the atp9 gene in CMS PET2, which led to the creation of two unique open reading frames orf288 and orf231. The first 53 bp of orf288 are identical to the 5' end of atp9. Orf231 consists apart from the first 3 bp, being part of the 271-bp-insertion, of the last 228 bp of atp9. These CMS PET2-specific orfs are co-transcribed. All 11 editing sites of the atp9 gene present in orf231 are fully edited. The anther-specific reduction of the co-transcript in fertility-restored hybrids supports the involvement in male-sterility based on CMS PET2.
Collapse
Affiliation(s)
- Antje Reddemann
- Institut für Biowissenschaften, Abt. Pflanzengenetik, Universität Rostock, Albert-Einstein-Straße 3, D-18059 Rostock, Germany
| | - Renate Horn
- Institut für Biowissenschaften, Abt. Pflanzengenetik, Universität Rostock, Albert-Einstein-Straße 3, D-18059 Rostock, Germany.
| |
Collapse
|
22
|
Kochetov AV, Glagoleva AY, Strygina KV, Khlestkina EK, Gerasimova SV, Ibragimova SM, Shatskaya NV, Vasilyev GV, Afonnikov DA, Shmakov NA, Antonova OY, Gavrilenko TA, Alpatyeva NV, Khiutti A, Afanasenko OS. Differential expression of NBS-LRR-encoding genes in the root transcriptomes of two Solanum phureja genotypes with contrasting resistance to Globodera rostochiensis. BMC PLANT BIOLOGY 2017; 17:251. [PMID: 29297325 PMCID: PMC5751396 DOI: 10.1186/s12870-017-1193-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
BACKGROUND The characterization of major resistance genes (R genes) in the potato remains an important task for molecular breeding. However, R genes are rapidly evolving and frequently occur in genomes as clusters with complex structures, and their precise mapping and identification are complicated and time consuming. RESULTS Comparative analysis of root transcriptomes of Solanum phureja genotypes with contrasting resistance to Globodera rostochiensis revealed a number of differentially expressed genes. However, compiling a list of candidate R genes for further segregation analysis was hampered by their scarce annotation. Nevertheless, combination of transcriptomic analysis with data on predicted potato NBS-LRR-encoding genes considerably improved the quality of the results and provided a reasonable number of candidate genes that provide S. phureja with strong resistance to the potato golden cyst nematode. CONCLUSION Combination of comparative analyses of tissue-specific transcriptomes in resistant and susceptible genotypes may be used as an approach for the rapid identification of candidate potato R genes for co-segregation analysis and may be used in parallel with more sophisticated studies based on genome resequencing.
Collapse
Affiliation(s)
- Alex V Kochetov
- Institute of Cytology and Genetics, SB RAS, Novosibirsk, 630090, Russia.
- Novosibirsk State University, Novosibirsk, 630090, Russia.
- Novosibirsk State Agrarian University, Novosibirsk, 630039, Russia.
| | - Anastasiya Y Glagoleva
- Institute of Cytology and Genetics, SB RAS, Novosibirsk, 630090, Russia
- Novosibirsk State University, Novosibirsk, 630090, Russia
| | | | - Elena K Khlestkina
- Institute of Cytology and Genetics, SB RAS, Novosibirsk, 630090, Russia
- Novosibirsk State University, Novosibirsk, 630090, Russia
| | | | | | | | | | | | - Nikolay A Shmakov
- Institute of Cytology and Genetics, SB RAS, Novosibirsk, 630090, Russia
| | - Olga Y Antonova
- Vavilov Institute of Plant Genetic Resources (VIR), Saint Petersburg, 190000, Russia
| | - Tatyana A Gavrilenko
- Vavilov Institute of Plant Genetic Resources (VIR), Saint Petersburg, 190000, Russia
- St. Petersburg State University, St. Petersburg, 199034, Russia
| | - Natalia V Alpatyeva
- Vavilov Institute of Plant Genetic Resources (VIR), Saint Petersburg, 190000, Russia
| | - Alexander Khiutti
- All Russian Research Institute for Plant Protection, Saint Petersburg, 196608, Russia
| | - Olga S Afanasenko
- All Russian Research Institute for Plant Protection, Saint Petersburg, 196608, Russia
| |
Collapse
|
23
|
Schönhals EM, Ortega F, Barandalla L, Aragones A, Ruiz de Galarreta JI, Liao JC, Sanetomo R, Walkemeier B, Tacke E, Ritter E, Gebhardt C. Identification and reproducibility of diagnostic DNA markers for tuber starch and yield optimization in a novel association mapping population of potato (Solanum tuberosum L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2016; 129:767-785. [PMID: 26825382 PMCID: PMC4799268 DOI: 10.1007/s00122-016-2665-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Accepted: 01/09/2016] [Indexed: 05/23/2023]
Abstract
SNPs in candidate genes Pain - 1, InvCD141 (invertases), SSIV (starch synthase), StCDF1 (transcription factor), LapN (leucine aminopeptidase), and cytoplasm type are associated with potato tuber yield, starch content and/or starch yield. Tuber yield (TY), starch content (TSC), and starch yield (TSY) are complex characters of high importance for the potato crop in general and for industrial starch production in particular. DNA markers associated with superior alleles of genes that control the natural variation of TY, TSC, and TSY could increase precision and speed of breeding new cultivars optimized for potato starch production. Diagnostic DNA markers are identified by association mapping in populations of tetraploid potato varieties and advanced breeding clones. A novel association mapping population of 282 genotypes including varieties, breeding clones and Andean landraces was assembled and field evaluated in Northern Spain for TY, TSC, TSY, tuber number (TN) and tuber weight (TW). The landraces had lower mean values of TY, TW, TN, and TSY. The population was genotyped for 183 microsatellite alleles, 221 single nucleotide polymorphisms (SNPs) in fourteen candidate genes and eight known diagnostic markers for TSC and TSY. Association test statistics including kinship and population structure reproduced five known marker-trait associations of candidate genes and discovered new ones, particularly for tuber yield and starch yield. The inclusion of landraces increased the number of detected marker-trait associations. Integration of the present association mapping results with previous QTL linkage mapping studies for TY, TSC, TSY, TW, TN, and tuberization revealed some hot spots of QTL for these traits in the potato genome. The genomic positions of markers linked or associated with QTL for complex tuber traits suggest high multiplicity and genome wide distribution of the underlying genes.
Collapse
Affiliation(s)
- E M Schönhals
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | | | | | | | | | - J-C Liao
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - R Sanetomo
- Potato Germplasm Enhancement Laboratory, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Japan
| | - B Walkemeier
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | | | | | - C Gebhardt
- Max Planck Institute for Plant Breeding Research, Cologne, Germany.
| |
Collapse
|