1
|
Sharma SK, McLean K, Hedley PE, Dale F, Daniels S, Bryan GJ. Genotyping-by-sequencing targets genic regions and improves resolution of genome-wide association studies in autotetraploid potato. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:180. [PMID: 38980417 PMCID: PMC11233353 DOI: 10.1007/s00122-024-04651-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 05/10/2024] [Indexed: 07/10/2024]
Abstract
KEY MESSAGE De novo genotyping in potato using methylation-sensitive GBS discovers SNPs largely confined to genic or gene-associated regions and displays enhanced effectiveness in estimating LD decay rates, population structure and detecting GWAS associations over 'fixed' SNP genotyping platform. Study also reports the genetic architectures including robust sequence-tagged marker-trait associations for sixteen important potato traits potentially carrying higher transferability across a wider range of germplasm. This study deploys recent advancements in polyploid analytical approaches to perform complex trait analyses in cultivated tetraploid potato. The study employs a 'fixed' SNP Infinium array platform and a 'flexible and open' genome complexity reduction-based sequencing method (GBS, genotyping-by-sequencing) to perform genome-wide association studies (GWAS) for several key potato traits including the assessment of population structure and linkage disequilibrium (LD) in the studied population. GBS SNPs discovered here were largely confined (~ 90%) to genic or gene-associated regions of the genome demonstrating the utility of using a methylation-sensitive restriction enzyme (PstI) for library construction. As compared to Infinium array SNPs, GBS SNPs displayed enhanced effectiveness in estimating LD decay rates and discriminating population subgroups. GWAS using a combined set of 30,363 SNPs identified 189 unique QTL marker-trait associations (QTL-MTAs) covering all studied traits. The majority of the QTL-MTAs were from GBS SNPs potentially illustrating the effectiveness of marker-dense de novo genotyping platforms in overcoming ascertainment bias and providing a more accurate correction for different levels of relatedness in GWAS models. GWAS also detected QTL 'hotspots' for several traits at previously known as well as newly identified genomic locations. Due to the current study exploiting genome-wide genotyping and de novo SNP discovery simultaneously on a large tetraploid panel representing a greater diversity of the cultivated potato gene pool, the reported sequence-tagged MTAs are likely to have higher transferability across a wider range of potato germplasm and increased utility for expediting genomics-assisted breeding for the several complex traits studied.
Collapse
Affiliation(s)
- Sanjeev Kumar Sharma
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK.
| | - Karen McLean
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | - Peter E Hedley
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | - Finlay Dale
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | | | - Glenn J Bryan
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK.
| |
Collapse
|
2
|
Pandey J, Thompson D, Joshi M, Scheuring DC, Koym JW, Joshi V, Vales MI. Genetic architecture of tuber-bound free amino acids in potato and effect of growing environment on the amino acid content. Sci Rep 2023; 13:13940. [PMID: 37626106 PMCID: PMC10457394 DOI: 10.1038/s41598-023-40880-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 08/17/2023] [Indexed: 08/27/2023] Open
Abstract
Free amino acids in potato tubers contribute to their nutritional value and processing quality. Exploring the natural variation in their accumulation in tubers across diverse genetic backgrounds is critical to potato breeding programs aiming to enhance or partition their distribution effectively. This study assessed variation in the tuber-bound free amino acids in a diversity panel of tetraploid potato clones developed and maintained by the Texas A&M Potato Breeding Program to explore their genetic basis and to obtain genomic-estimated breeding values for applied breeding purposes. Free amino acids content was evaluated in tubers of 217 tetraploid potato clones collected from Dalhart, Texas in 2019 and 2020, and Springlake, Texas in 2020. Most tuber amino acids were not affected by growing location, except histidine and proline, which were significantly lower (- 59.0%) and higher (+ 129.0%), respectively, at Springlake, Texas (a location that regularly suffers from abiotic stresses, mainly high-temperature stress). Single nucleotide polymorphism markers were used for genome-wide association studies and genomic selection of clones based on amino acid content. Most amino acids showed significant variations among potato clones and moderate to high heritabilities. Principal component analysis separated fresh from processing potato market classes based on amino acids distribution patterns. Genome-wide association studies discovered 33 QTL associated with 13 free amino acids. Genomic-estimated breeding values were calculated and are recommended for practical potato breeding applications to select parents and advance clones with the desired free amino acid content.
Collapse
Affiliation(s)
- Jeewan Pandey
- Department of Horticultural Sciences, Texas A&M University, College Station, TX, 77843, USA
| | - Dalton Thompson
- Texas A&M AgriLife Research and Extension Center, Uvalde, TX, 78801, USA
| | - Madhumita Joshi
- Texas A&M AgriLife Research and Extension Center, Uvalde, TX, 78801, USA
| | - Douglas C Scheuring
- Department of Horticultural Sciences, Texas A&M University, College Station, TX, 77843, USA
| | - Jeffrey W Koym
- Texas A&M AgriLife Research and Extension Center, Lubbock, TX, 79403, USA
| | - Vijay Joshi
- Department of Horticultural Sciences, Texas A&M University, College Station, TX, 77843, USA.
- Texas A&M AgriLife Research and Extension Center, Uvalde, TX, 78801, USA.
| | - M Isabel Vales
- Department of Horticultural Sciences, Texas A&M University, College Station, TX, 77843, USA.
| |
Collapse
|
3
|
Tatarowska B, Milczarek D, Plich J. The Content of Total Carotenoids, Vitamin C and Antioxidant Properties of 65 Potato Cultivars Characterised under the European Project ECOBREED. Int J Mol Sci 2023; 24:11716. [PMID: 37511473 PMCID: PMC10380281 DOI: 10.3390/ijms241411716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 07/13/2023] [Accepted: 07/14/2023] [Indexed: 07/30/2023] Open
Abstract
The aim of this study was to determine the effect of cultivars on the concentration of antioxidant compounds: total carotenoid content (TC) and vitamin C (VC), and their correlation with the total antioxidant activity (TAA) in 65 potato cultivars (Solanum tuberosum) from 10 countries. The TC content revealed a highly significant effect of the year (Y), cultivar (C) and flesh colour (FC). The TC ranged from 101.5 µg 100 g-1 DM (in cv. Kelly) to 715 µg 100 g-1 DM (in cv. Mayan Gold). The TC values were weakly correlated with years and higher in yellow-fleshed potatoes than in white-fleshed potatoes (319.9 vs. 175.6 µg 100 g-1 DM, respectively). The VC content ranged from 1.0 mg 100 g-1 FM (in cv. Bzura) to 14.8 mg 100 g-1 FM (in cv. Twinner). The content of VC were higher in yellow-fleshed (6.5 mg 100 g-1 FM) than in white-fleshed potatoes (5.8 mg 100 g-1 FM). The highest TAA were observed in cvs. Colleen, Basa, Triplo, Gatsby, Ditta, Twinner, Riviera, Michalina, Damaris, Belmonda, Ambo, Savinja, 12-LHI-6. For these cultivars, the FRAP values were 0.53 µmol TE 100 mg-1 DM and DPPH 0.55 µmol TE 100 mg-1 DM. The lowest TAA were observed in cvs.: Owacja, Mayan Gold, Kokra, Magnolia and Kelly. For them, the FRAP and DPPH values were slightly above 0.2 µmol TE 100 mg-1 DM. It was shown that the concentration of TC in potato tubers has an impact on TAA.
Collapse
Affiliation(s)
- Beata Tatarowska
- Plant Breeding and Acclimatization Institute-National Research Institute in Radzików, Młochów Division, Department of Potato Genetics and Parental Lines, Platanowa Str. 19, 05-831 Młochów, Poland
| | - Dorota Milczarek
- Plant Breeding and Acclimatization Institute-National Research Institute in Radzików, Młochów Division, Department of Potato Genetics and Parental Lines, Platanowa Str. 19, 05-831 Młochów, Poland
| | - Jarosław Plich
- Plant Breeding and Acclimatization Institute-National Research Institute in Radzików, Młochów Division, Department of Potato Genetics and Parental Lines, Platanowa Str. 19, 05-831 Młochów, Poland
| |
Collapse
|
4
|
Chincinska IA, Miklaszewska M, Sołtys-Kalina D. Recent advances and challenges in potato improvement using CRISPR/Cas genome editing. PLANTA 2022; 257:25. [PMID: 36562862 PMCID: PMC9789015 DOI: 10.1007/s00425-022-04054-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Accepted: 12/11/2022] [Indexed: 06/17/2023]
Abstract
MAIN CONCLUSION Genome editing using CRISPR/Cas technology improves the quality of potato as a food crop and enables its use as both a model plant in fundamental research and as a potential biofactory for producing valuable compounds for industrial applications. Potato (Solanum tuberosum L.) plays a significant role in ensuring global food and nutritional security. Tuber yield is negatively affected by biotic and abiotic stresses, and enzymatic browning and cold-induced sweetening significantly contribute to post-harvest quality losses. With the dual challenges of a growing population and a changing climate, potato enhancement is essential for its sustainable production. However, due to several characteristics of potato, including high levels of heterozygosity, tetrasomic inheritance, inbreeding depression, and self-incompatibility of diploid potato, conventional breeding practices are insufficient to achieve substantial trait improvement in tetraploid potato cultivars within a relatively short time. CRISPR/Cas-mediated genome editing has opened new possibilities to develop novel potato varieties with high commercialization potential. In this review, we summarize recent developments in optimizing CRISPR/Cas-based methods for potato genome editing, focusing on approaches addressing the challenging biology of this species. We also discuss the feasibility of obtaining transgene-free genome-edited potato varieties and explore different strategies to improve potato stress resistance, nutritional value, starch composition, and storage and processing characteristics. Altogether, this review provides insight into recent advances, possible bottlenecks, and future research directions in potato genome editing using CRISPR/Cas technology.
Collapse
Affiliation(s)
- Izabela Anna Chincinska
- Department of Plant Physiology and Biotechnology, University of Gdańsk, Wita Stwosza 59, 80-308, Gdańsk, Poland.
| | - Magdalena Miklaszewska
- Department of Functional and Evolutionary Ecology, Division of Molecular Systems Biology (MOSYS), Faculty of Life Sciences, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria
| | - Dorota Sołtys-Kalina
- Plant Breeding and Acclimatization Institute-National Research Institute, Platanowa 19, 05-831, Młochów, Poland
| |
Collapse
|
5
|
Pandey J, Scheuring DC, Koym JW, Vales MI. Genomic regions associated with tuber traits in tetraploid potatoes and identification of superior clones for breeding purposes. FRONTIERS IN PLANT SCIENCE 2022; 13:952263. [PMID: 35937326 PMCID: PMC9354404 DOI: 10.3389/fpls.2022.952263] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 06/29/2022] [Indexed: 05/05/2023]
Abstract
In potato breeding, morphological tuber traits are important selection targets to meet the demands of the fresh and processing markets. Understanding the genetic basis of tuber traits should guide selection and improve breeding efficiencies. However, this is challenging in potato due to the complexity of the traits and the polyploid nature of the potato genome. High-throughput affordable molecular markers and new software specific for polyploid species have the potential to unlock previously unattainable levels of understanding of the genetic basis of tuber traits in tetraploid potato. In this study, we genotyped a diversity panel of 214 advanced clones with the 22 K SNP potato array and phenotyped it in three field environments in Texas. We conducted a genome-wide association study using the GWASpoly software package to identify genomic regions associated with tuber morphological traits. Some of the QTLs discovered confirmed prior studies, whereas others were discovered for the first time. The main QTL for tuber shape was detected on chromosome 10 and explained 5.8% of the phenotypic variance. GWAS analysis of eye depth detected a significant QTL on chromosome 10 and explained 3.9% of the phenotypic variance. Another QTL peak for eye depth on chromosome 5 was located near the CDF1 gene, an important regulator of maturity in potato. Our study found that multiple QTLs govern russeting in potato. A major QTL for flesh color on chromosome 3 that explained 26% of the phenotypic variance likely represents the Y locus responsible for yellow flesh in potato tubers. Several QTLs were detected for purple skin color on chromosome 11. Furthermore, genomic estimated breeding values were obtained, which will aid in the early identification of superior parental clones that should increase the chances of producing progenies with higher frequencies of the desired tuber traits. These findings will contribute to a better understanding of the genetic basis of morphological traits in potato, as well as to identifying parents with the best breeding values to improve selection efficiency in our potato breeding program.
Collapse
Affiliation(s)
- Jeewan Pandey
- Department of Horticultural Sciences, Texas A&M University, College Station, TX, United States
| | - Douglas C. Scheuring
- Department of Horticultural Sciences, Texas A&M University, College Station, TX, United States
| | - Jeffrey W. Koym
- Texas A&M University AgriLife Research and Extension Center, Lubbock, TX, United States
| | - M. Isabel Vales
- Department of Horticultural Sciences, Texas A&M University, College Station, TX, United States
| |
Collapse
|
6
|
Tang D, Jia Y, Zhang J, Li H, Cheng L, Wang P, Bao Z, Liu Z, Feng S, Zhu X, Li D, Zhu G, Wang H, Zhou Y, Zhou Y, Bryan GJ, Buell CR, Zhang C, Huang S. Genome evolution and diversity of wild and cultivated potatoes. Nature 2022; 606:535-541. [PMID: 35676481 PMCID: PMC9200641 DOI: 10.1038/s41586-022-04822-x] [Citation(s) in RCA: 108] [Impact Index Per Article: 54.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 04/28/2022] [Indexed: 12/21/2022]
Abstract
Potato (Solanum tuberosum L.) is the world's most important non-cereal food crop, and the vast majority of commercially grown cultivars are highly heterozygous tetraploids. Advances in diploid hybrid breeding based on true seeds have the potential to revolutionize future potato breeding and production1-4. So far, relatively few studies have examined the genome evolution and diversity of wild and cultivated landrace potatoes, which limits the application of their diversity in potato breeding. Here we assemble 44 high-quality diploid potato genomes from 24 wild and 20 cultivated accessions that are representative of Solanum section Petota, the tuber-bearing clade, as well as 2 genomes from the neighbouring section, Etuberosum. Extensive discordance of phylogenomic relationships suggests the complexity of potato evolution. We find that the potato genome substantially expanded its repertoire of disease-resistance genes when compared with closely related seed-propagated solanaceous crops, indicative of the effect of tuber-based propagation strategies on the evolution of the potato genome. We discover a transcription factor that determines tuber identity and interacts with the mobile tuberization inductive signal SP6A. We also identify 561,433 high-confidence structural variants and construct a map of large inversions, which provides insights for improving inbred lines and precluding potential linkage drag, as exemplified by a 5.8-Mb inversion that is associated with carotenoid content in tubers. This study will accelerate hybrid potato breeding and enrich our understanding of the evolution and biology of potato as a global staple food crop.
Collapse
Affiliation(s)
- Dié Tang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Yuxin Jia
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Jinzhe Zhang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hongbo Li
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.,Graduate School Experimental Plant Sciences, Laboratory of Plant Breeding, Wageningen University and Research, Wageningen, The Netherlands
| | - Lin Cheng
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Pei Wang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Zhigui Bao
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Zhihong Liu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Shuangshuang Feng
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xijian Zhu
- The AGISCAAS-YNNU Joint Academy of Potato Sciences, Yunnan Normal University, Kunming, China
| | - Dawei Li
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Guangtao Zhu
- The AGISCAAS-YNNU Joint Academy of Potato Sciences, Yunnan Normal University, Kunming, China
| | - Hongru Wang
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA, USA
| | - Yao Zhou
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Yongfeng Zhou
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Glenn J Bryan
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, UK
| | - C Robin Buell
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, USA
| | - Chunzhi Zhang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Sanwen Huang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
| |
Collapse
|
7
|
Fine Mapping and Candidate Gene Prediction of Tuber Shape Controlling Ro Locus Based on Integrating Genetic and Transcriptomic Analyses in Potato. Int J Mol Sci 2022; 23:ijms23031470. [PMID: 35163389 PMCID: PMC8836246 DOI: 10.3390/ijms23031470] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 01/25/2022] [Accepted: 01/26/2022] [Indexed: 12/10/2022] Open
Abstract
Tuber shape is one of the most important quality traits in potato appearance. Since poor or irregular shape results in higher costs for processing and influences the consumers’ willingness to purchase, breeding for shape uniformity and shallow eye depth is highly important. Previous studies showed that the major round tuber shape controlling locus, the Ro locus, is located on chromosome 10. However, fine mapping and cloning of tuber shape genes have not been reported. In this study, the analyses of tissue sectioning and transcriptome sequencing showed that the developmental differences between round and elongated tuber shapes begin as early as the hook stage of the stolon. To fine map tuber shape genes, a high-density genetic linkage map of the Ro region on chromosome 10 based on a diploid segregating population was constructed. The total length of the genetic linkage map was 25.8 cM and the average marker interval was 1.98 cM. Combined with phenotypic data collected from 2014 to 2017, one major quantitative trait locus (QTL) for tuber shape was identified, which explained 61.7–72.9% of the tuber shape variation. Through the results of genotyping and phenotypic investigation of recombinant individuals, Ro was fine mapped in a 193.43 kb interval, which contained 18 genes. Five candidate genes were preliminarily predicted based on tissue sections and transcriptome sequencing. This study provides an important basis for cloning Ro gene(s).
Collapse
|
8
|
Zhang C, Yang Z, Tang D, Zhu Y, Wang P, Li D, Zhu G, Xiong X, Shang Y, Li C, Huang S. Genome design of hybrid potato. Cell 2021; 184:3873-3883.e12. [PMID: 34171306 DOI: 10.1016/j.cell.2021.06.006] [Citation(s) in RCA: 70] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 04/01/2021] [Accepted: 06/02/2021] [Indexed: 12/15/2022]
Abstract
Reinventing potato from a clonally propagated tetraploid into a seed-propagated diploid, hybrid potato, is an important innovation in agriculture. Due to deleterious mutations, it has remained a challenge to develop highly homozygous inbred lines, a prerequisite to breed hybrid potato. Here, we employed genome design to develop a generation of pure and fertile potato lines and thereby the uniform, vigorous F1s. The metrics we applied in genome design included the percentage of genome homozygosity and the number of deleterious mutations in the starting material, the number of segregation distortions in the S1 population, the haplotype information to infer the break of tight linkage between beneficial and deleterious alleles, and the genome complementarity of the parental lines. This study transforms potato breeding from a slow, non-accumulative mode into a fast-iterative one, thereby potentiating a broad spectrum of benefits to farmers and consumers.
Collapse
Affiliation(s)
- Chunzhi Zhang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China
| | - Zhongmin Yang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China
| | - Dié Tang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China
| | - Yanhui Zhu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China
| | - Pei Wang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China
| | - Dawei Li
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China
| | - Guangtao Zhu
- The AGISCAAS-YNNU Joint Academy of Potato Sciences, Yunnan Normal University, Kunming, Yunnan 650500, China
| | - Xingyao Xiong
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China
| | - Yi Shang
- The AGISCAAS-YNNU Joint Academy of Potato Sciences, Yunnan Normal University, Kunming, Yunnan 650500, China
| | - Canhui Li
- The AGISCAAS-YNNU Joint Academy of Potato Sciences, Yunnan Normal University, Kunming, Yunnan 650500, China
| | - Sanwen Huang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China.
| |
Collapse
|
9
|
Pandey J, Scheuring DC, Koym JW, Coombs J, Novy RG, Thompson AL, Holm DG, Douches DS, Miller JC, Vales MI. Genetic diversity and population structure of advanced clones selected over forty years by a potato breeding program in the USA. Sci Rep 2021; 11:8344. [PMID: 33863959 PMCID: PMC8052460 DOI: 10.1038/s41598-021-87284-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 03/24/2021] [Indexed: 01/12/2023] Open
Abstract
Knowledge regarding genetic diversity and population structure of breeding materials is essential for crop improvement. The Texas A&M University Potato Breeding Program has a collection of advanced clones selected and maintained in-vitro over a 40-year period. Little is known about its genetic makeup and usefulness for the current breeding program. In this study, 214 potato clones were genotyped with the Infinium Illumina 22 K V3 Potato Array. After filtering, a total of 10,106 single nucleotide polymorphic (SNP) markers were used for analysis. Heterozygosity varied by SNP, with an overall average of 0.59. Three groups of tetraploid clones primarily based on potato market classes, were detected using STRUCTURE software and confirmed by discriminant analysis of principal components.
The highest coefficient of differentiation observed between the groups was 0.14. Signatures of selection were uncovered in genes controlling potato flesh and skin color, length of plant cycle and tuberization, and carbohydrate metabolism. A core set of 43 clones was obtained using Core Hunter 3 to develop a sub-collection that retains similar genetic diversity as the whole population, minimize redundancies, and facilitates long-term conservation of genetic resources. The comprehensive molecular characterization of our breeding clone bank collection contributes to understanding the genetic diversity of existing potato resources. This analysis could be applied to other breeding programs and assist in the selection of parents, fingerprinting, protection, and management of the breeding collections.
Collapse
Affiliation(s)
- Jeewan Pandey
- Department of Horticultural Sciences, Texas A&M University, College Station, TX, 77843-2133, USA
| | - Douglas C Scheuring
- Department of Horticultural Sciences, Texas A&M University, College Station, TX, 77843-2133, USA
| | - Jeffrey W Koym
- Texas A&M AgriLife Research and Extension Center, Lubbock, TX, 79403, USA
| | - Joseph Coombs
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI, 48824, USA
| | - Richard G Novy
- USDA-Agricultural Research Service, Small Grains and Potato Germplasm Research, Aberdeen, ID, 83210, USA
| | - Asunta L Thompson
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA
| | - David G Holm
- San Luis Valley Research Center, Department of Horticulture and Landscape Architecture, Colorado State University, Center, CO, 81125, USA
| | - David S Douches
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI, 48824, USA
| | - J Creighton Miller
- Department of Horticultural Sciences, Texas A&M University, College Station, TX, 77843-2133, USA
| | - M Isabel Vales
- Department of Horticultural Sciences, Texas A&M University, College Station, TX, 77843-2133, USA.
| |
Collapse
|
10
|
eQTL mapping of the 12S globulin cruciferin gene PGCRURSE5 as a novel candidate associated with starch content in potato tubers. Sci Rep 2020; 10:17168. [PMID: 33051578 PMCID: PMC7553954 DOI: 10.1038/s41598-020-74285-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 09/30/2020] [Indexed: 11/09/2022] Open
Abstract
Tuber starch content (TSC) is a very important trait in potato (Solanum tuberosum L.). This study is the first to use expression quantitative trait loci (eQTL) mapping of transcript-derived markers for TSC in potato. Thirty-four differentially expressed genes were selected by comparing the RNA-seq data of contrasting bulked segregants. For the 11 candidate genes, we determined their relative expression levels across the segregating diploid potato population using RT-qPCR. We detected 36 eQTL as candidate genes distributed on all twelve potato chromosomes, and nine of them overlapped with QTL for TSC. Peaks for two eQTL, eAGPaseS-a and ePGRCRURSE5, were close to the corresponding loci of the large subunit of ADP-glucose pyrophosphorylase (AGPaseS-a) and the 12S globulin cruciferin gene (PGCRURSE5), respectively. The eQTL peaks for AGPaseS-a and PGRCRURSE5 explained 41.0 and 28.3% of the phenotypic variation at the transcript level. We showed the association of the DNA markers for AGPaseS-a and PGRCRURSE5 with QTL for TSC, and significant correlation between the expression level of PGRCRURSE5 and TSC. We did not observe a significant correlation between the expression level of AGPaseS-a and TSC. We concluded that the cruciferin gene PGRCRURSE5 is a novel candidate involved in the regulation of starch content in potato tubers.
Collapse
|
11
|
Nguyen KL, Grondin A, Courtois B, Gantet P. Next-Generation Sequencing Accelerates Crop Gene Discovery. TRENDS IN PLANT SCIENCE 2019; 24:263-274. [PMID: 30573308 DOI: 10.1016/j.tplants.2018.11.008] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 11/20/2018] [Accepted: 11/22/2018] [Indexed: 05/22/2023]
Abstract
The identification and isolation of genes underlying quantitative trait loci (QTLs) associated with agronomic traits in crops have been recently accelerated thanks to next-generation sequencing (NGS)-based technologies combined with plant genetics. With NGS, various revisited genetic approaches, which benefited from higher marker density, have been elaborated. These approaches improved resolution in QTL position and assisted in determining functional causative variations in genes. Examples of QTLs/genes associated with agronomic traits in crops and identified using different strategies based on whole-genome sequencing (WGS)/whole-genome resequencing (WGR) or RNA-seq are presented and discussed in this review. More specifically, we summarize and illustrate how NGS boosted bulk-segregant analysis (BSA), expression profiling, and the construction of polymorphism databases to facilitate the detection of QTLs and causative genes.
Collapse
Affiliation(s)
- Khanh Le Nguyen
- Université de Montpellier, Institut de Recherche pour le Développement, UMR DIADE, 911 Avenue Agropolis, 34394 Montpellier cedex 5, France; LMI RICE 2, AGI, Km2 Pham Van Dong, Tu Liem, Hanoi, Vietnam
| | - Alexandre Grondin
- Université de Montpellier, Institut de Recherche pour le Développement, UMR DIADE, 911 Avenue Agropolis, 34394 Montpellier cedex 5, France
| | - Brigitte Courtois
- CIRAD, UMR AGAP, F-34398 Montpellier, France; Université de Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Pascal Gantet
- Université de Montpellier, Institut de Recherche pour le Développement, UMR DIADE, 911 Avenue Agropolis, 34394 Montpellier cedex 5, France; Centre of the Region Haná for Biotechnological and Agricultural Research, Dept. of Molecular Biology, Faculty of Science, Palacký University, Olomouc, Czech Republic.
| |
Collapse
|
12
|
Sharma SK, MacKenzie K, McLean K, Dale F, Daniels S, Bryan GJ. Linkage Disequilibrium and Evaluation of Genome-Wide Association Mapping Models in Tetraploid Potato. G3 (BETHESDA, MD.) 2018; 8:3185-3202. [PMID: 30082329 PMCID: PMC6169395 DOI: 10.1534/g3.118.200377] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 07/30/2018] [Indexed: 11/18/2022]
Abstract
Genome-wide association studies (GWAS) have become a powerful tool for analyzing complex traits in crop plants. The current study evaluates the efficacy of various GWAS models and methods for elucidating population structure in potato. The presence of significant population structure can lead to detection of spurious marker-trait associations, as well as mask true ones. While appropriate statistical models are needed to detect true marker-trait associations, in most published potato GWAS, a 'one model fits all traits' approach has been adopted. We have examined various GWAS models on a large association panel comprising diverse tetraploid potato cultivars and breeding lines, genotyped with single nucleotide polymorphism (SNP) markers. Phenotypic data were generated for 20 quantitative traits assessed in different environments. Best Linear Unbiased Estimates (BLUEs) for these traits were obtained for use in assessing GWAS models. Goodness of fit of GWAS models, derived using different combinations of kinship and population structure for all traits, was evaluated using Quantile-Quantile (Q-Q) plots and genomic control inflation factors (λGC). Kinship was found to play a major role in correcting population confounding effects and results advocate a 'trait-specific' fit of different GWAS models. A survey of genome-wide linkage disequilibrium (LD), one of the critical factors affecting GWAS, is also presented and our findings are compared to other recent studies in potato. The genetic material used here, and the outputs of this study represent a novel resource for genetic analysis in potato.
Collapse
Affiliation(s)
| | - Katrin MacKenzie
- Biomathematics and Statistics Scotland (BioSS), Dundee DD2 5DA, UK
| | | | - Finlay Dale
- The James Hutton Institute, Dundee DD2 5DA, UK
| | | | | |
Collapse
|
13
|
Sprenger H, Erban A, Seddig S, Rudack K, Thalhammer A, Le MQ, Walther D, Zuther E, Köhl KI, Kopka J, Hincha DK. Metabolite and transcript markers for the prediction of potato drought tolerance. PLANT BIOTECHNOLOGY JOURNAL 2018; 16:939-950. [PMID: 28929574 PMCID: PMC5866952 DOI: 10.1111/pbi.12840] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Revised: 09/07/2017] [Accepted: 09/12/2017] [Indexed: 05/13/2023]
Abstract
Potato (Solanum tuberosum L.) is one of the most important food crops worldwide. Current potato varieties are highly susceptible to drought stress. In view of global climate change, selection of cultivars with improved drought tolerance and high yield potential is of paramount importance. Drought tolerance breeding of potato is currently based on direct selection according to yield and phenotypic traits and requires multiple trials under drought conditions. Marker-assisted selection (MAS) is cheaper, faster and reduces classification errors caused by noncontrolled environmental effects. We analysed 31 potato cultivars grown under optimal and reduced water supply in six independent field trials. Drought tolerance was determined as tuber starch yield. Leaf samples from young plants were screened for preselected transcript and nontargeted metabolite abundance using qRT-PCR and GC-MS profiling, respectively. Transcript marker candidates were selected from a published RNA-Seq data set. A Random Forest machine learning approach extracted metabolite and transcript markers for drought tolerance prediction with low error rates of 6% and 9%, respectively. Moreover, by combining transcript and metabolite markers, the prediction error was reduced to 4.3%. Feature selection from Random Forest models allowed model minimization, yielding a minimal combination of only 20 metabolite and transcript markers that were successfully tested for their reproducibility in 16 independent agronomic field trials. We demonstrate that a minimum combination of transcript and metabolite markers sampled at early cultivation stages predicts potato yield stability under drought largely independent of seasonal and regional agronomic conditions.
Collapse
Affiliation(s)
- Heike Sprenger
- Max‐Planck‐Institute of Molecular Plant PhysiologyPotsdamGermany
- Present address:
VIB‐UGent Center for Plant Systems BiologyTechnologiepark 9279052GhentBelgium
| | - Alexander Erban
- Max‐Planck‐Institute of Molecular Plant PhysiologyPotsdamGermany
| | - Sylvia Seddig
- Federal Research Centre for Cultivated PlantsJulius‐Kühn InstitutInstitute for Resistance Research and Stress ToleranceSanitzGermany
| | - Katharina Rudack
- Federal Research Centre for Cultivated PlantsJulius‐Kühn InstitutInstitute for Resistance Research and Stress ToleranceSanitzGermany
| | - Anja Thalhammer
- Max‐Planck‐Institute of Molecular Plant PhysiologyPotsdamGermany
- Present address:
University of PotsdamKarl‐Liebknecht‐Straße 24‐2514476PotsdamGermany
| | - Mai Q. Le
- VNU‐University of SciencesThanh XuanHanoiVietnam
| | - Dirk Walther
- Max‐Planck‐Institute of Molecular Plant PhysiologyPotsdamGermany
| | - Ellen Zuther
- Max‐Planck‐Institute of Molecular Plant PhysiologyPotsdamGermany
| | - Karin I. Köhl
- Max‐Planck‐Institute of Molecular Plant PhysiologyPotsdamGermany
| | - Joachim Kopka
- Max‐Planck‐Institute of Molecular Plant PhysiologyPotsdamGermany
| | - Dirk K. Hincha
- Max‐Planck‐Institute of Molecular Plant PhysiologyPotsdamGermany
| |
Collapse
|
14
|
Hara-Skrzypiec A, Śliwka J, Jakuczun H, Zimnoch-Guzowska E. QTL for tuber morphology traits in diploid potato. J Appl Genet 2018; 59:123-132. [PMID: 29492845 PMCID: PMC5895667 DOI: 10.1007/s13353-018-0433-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 02/07/2018] [Accepted: 02/08/2018] [Indexed: 11/24/2022]
Abstract
A diploid, potato mapping population consisting of 149 individuals was assessed in three consecutive years for important agronomic and quality traits: tuber shape, regularity of tuber shape, eye depth, mean tuber weight, and tuber flesh color. Analysis of variance showed that the genotype had the largest influence on the phenotypic scores but effect of the genotype × year interactions was also strong. Using this data and an existing genetic map, a quantitative trait loci (QTL) analysis was conducted. From four to seven QTL were detected for each trait except tuber flesh color, which was determined by a major QTL on chromosome III explaining 76.8% of the trait variance. Additionally, a minor QTL for flesh color was localized on chromosome II. For the other traits, significant QTL were detected: for tuber shape on chromosome X, for regularity of tuber shape on chromosome III, for eye depth on chromosome IV, and for tuber weight on chromosome I. Some detected QTL confirmed previous studies, but new ones were also identified.
Collapse
Affiliation(s)
- Agnieszka Hara-Skrzypiec
- Plant Breeding and Acclimatization Institute - National Research Institute, Platanowa 19, 05-831, Młochów, Poland.
| | - J Śliwka
- Plant Breeding and Acclimatization Institute - National Research Institute, Platanowa 19, 05-831, Młochów, Poland
| | - H Jakuczun
- Plant Breeding and Acclimatization Institute - National Research Institute, Platanowa 19, 05-831, Młochów, Poland
| | - E Zimnoch-Guzowska
- Plant Breeding and Acclimatization Institute - National Research Institute, Platanowa 19, 05-831, Młochów, Poland
| |
Collapse
|
15
|
Acharjee A, Chibon PY, Kloosterman B, America T, Renaut J, Maliepaard C, Visser RGF. Genetical genomics of quality related traits in potato tubers using proteomics. BMC PLANT BIOLOGY 2018; 18:20. [PMID: 29361908 PMCID: PMC5781343 DOI: 10.1186/s12870-018-1229-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 01/09/2018] [Indexed: 05/21/2023]
Abstract
BACKGROUND Recent advances in ~omics technologies such as transcriptomics, metabolomics and proteomics along with genotypic profiling have permitted the genetic dissection of complex traits such as quality traits in non-model species. To get more insight into the genetic factors underlying variation in quality traits related to carbohydrate and starch metabolism and cold sweetening, we determined the protein content and composition in potato tubers using 2D-gel electrophoresis in a diploid potato mapping population. Upon analyzing we made sure that the proteins from the patatin family were excluded to ensure a better representation of the other proteins. RESULTS We subsequently performed pQTL analyses for all other proteins with a sufficient representation in the population and established a relationship between proteins and 26 potato tuber quality traits (e.g. flesh colour, enzymatic discoloration) by co-localization on the genetic map and a direct correlation study of protein abundances and phenotypic traits. Over 1643 unique protein spots were detected in total over the two harvests. We were able to map pQTLs for over 300 different protein spots some of which co-localized with traits such as starch content and cold sweetening. pQTLs were observed on every chromosome although not evenly distributed over the chromosomes. The largest number of pQTLs was found for chromosome 8 and the lowest for chromosome number 10. For some 20 protein spots multiple QTLs were observed. CONCLUSIONS From this analysis, hotspot areas for protein QTLs were identified on chromosomes three, five, eight and nine. The hotspot on chromosome 3 coincided with a QTL previously identified for total protein content and had more than 23 pQTLs in the region from 70 to 80 cM. Some of the co-localizing protein spots associated with some of the most interesting tuber quality traits were identified, albeit far less than we had anticipated at the onset of the experiments.
Collapse
Affiliation(s)
- Animesh Acharjee
- Graduate School Experimental Plant Sciences, Wageningen, The Netherlands
- Plant Breeding, Wageningen University and Research, PO Box 386, 6700 AJ Wageningen, The Netherlands
- Institute of Cancer and Genomic Sciences, Centre for Computational Biology, University of Birmingham, Birmingham, B15 2TT UK
- Institute of Translational Medicine, University Hospitals Birmingham NHS Foundation Trust, Birmingham, B15 2TT UK
| | - Pierre-Yves Chibon
- Graduate School Experimental Plant Sciences, Wageningen, The Netherlands
- Plant Breeding, Wageningen University and Research, PO Box 386, 6700 AJ Wageningen, The Netherlands
| | - Bjorn Kloosterman
- Plant Breeding, Wageningen University and Research, PO Box 386, 6700 AJ Wageningen, The Netherlands
- Present address: Keygene NV, PO Box 216, 6700 AE Wageningen, The Netherlands
| | - Twan America
- Centre for BioSystems Genomics, P.O. Box 98, 6700 AA Wageningen, The Netherlands
- Business unit BiosciencesWageningen University and Research, P.O. Box 16, 6700 AA Wageningen, The Netherlands
| | - Jenny Renaut
- Centre de Recherche Public - Gabriel Lippmann Department of Environment and Agrobiotechnologies (EVA) 41, rue du Brill, L-4422 Belvaux, Luxembourg
| | - Chris Maliepaard
- Plant Breeding, Wageningen University and Research, PO Box 386, 6700 AJ Wageningen, The Netherlands
| | - Richard G. F. Visser
- Plant Breeding, Wageningen University and Research, PO Box 386, 6700 AJ Wageningen, The Netherlands
- Centre for BioSystems Genomics, P.O. Box 98, 6700 AA Wageningen, The Netherlands
| |
Collapse
|
16
|
Hara-Skrzypiec A, Śliwka J, Jakuczun H, Zimnoch-Guzowska E. Quantitative trait loci for tuber blackspot bruise and enzymatic discoloration susceptibility in diploid potato. Mol Genet Genomics 2017; 293:331-342. [PMID: 29080143 PMCID: PMC5854731 DOI: 10.1007/s00438-017-1387-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 10/19/2017] [Indexed: 12/19/2022]
Abstract
Tuber tissue discolorations caused by impact (blackspot bruising) and enzymatic discoloration (ED) after tuber cutting are crucial quality traits of the cultivated potato. To understand the complex genetics of the traits, quantitative trait locus (QTL) analysis using diploid mapping population and diversity array technology (DArT) markers was performed. The phenotypic assessment included the complex evaluation of blackspot bruising susceptibility through two methods: rotating drum (BRD) and falling bolt (BFB) in combination with the evaluation of enzymatic discoloration. Because of observed in-practice relationship between bruising susceptibility and tuber starch content (TSC), analysis of starch content-corrected bruising susceptibility (SCB) was performed. QTLs for bruising were detected on chromosomes I, V with both test methods. The rotating drum method enabled the detection of additional QTLs on chromosomes VIII and XII. Analysis of SCB enabled the identification of the major QTL on chromosome V and two weaker QTLs on chromosomes VIII and XII, independently of starch content. The QTL for bruising detected on chromosome I overlapped with the most significant QTL for tuber starch content. This QTL was not significant for starch content-corrected bruising susceptibility, and the effect of the QTL on chromosome V was enhanced for this trait. The QTL analysis of ED revealed the contribution of seven QTLs for the trait, located on six chromosomes, including these detected for the first time: a major locus on chromosome V and minor QTLs on chromosomes VII and X, which were specific for the trait. The QTL for ED on chromosome VIII was co-localized with the marker for polyphenol oxidase (POT32). The phenotypic correlation between bruising and ED was confirmed in QTL analyses of both traits, and the QTLs detected for these traits overlapped on chromosomes I, V, and VIII. Our results should provide a basis for further studies on candidate genes affecting blackspot bruise susceptibility and enzymatic discoloration.
Collapse
Affiliation(s)
- Agnieszka Hara-Skrzypiec
- Plant Breeding and Acclimatization Institute, National Research Institute, Młochów, Platanowa 19, 05-831, Młochów, Poland.
| | - J Śliwka
- Plant Breeding and Acclimatization Institute, National Research Institute, Młochów, Platanowa 19, 05-831, Młochów, Poland
| | - H Jakuczun
- Plant Breeding and Acclimatization Institute, National Research Institute, Młochów, Platanowa 19, 05-831, Młochów, Poland
| | - E Zimnoch-Guzowska
- Plant Breeding and Acclimatization Institute, National Research Institute, Młochów, Platanowa 19, 05-831, Młochów, Poland
| |
Collapse
|
17
|
Sulli M, Mandolino G, Sturaro M, Onofri C, Diretto G, Parisi B, Giuliano G. Molecular and biochemical characterization of a potato collection with contrasting tuber carotenoid content. PLoS One 2017; 12:e0184143. [PMID: 28898255 PMCID: PMC5595298 DOI: 10.1371/journal.pone.0184143] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 08/18/2017] [Indexed: 12/26/2022] Open
Abstract
After wheat and rice, potato is the third most important staple food worldwide. A collection of ten tetraploid (Solanum tuberosum) and diploid (S. phureja and S. chacoense) genotypes with contrasting carotenoid content was subjected to molecular characterization with respect to candidate carotenoid loci and metabolic profiling using LC-HRMS. Irrespective of ploidy and taxonomy, tubers of these genotypes fell into three groups: yellow-fleshed, characterized by high levels of epoxy-xanthophylls and xanthophyll esters and by the presence of at least one copy of a dominant allele of the β-Carotene Hydroxylase 2 (CHY2) gene; white-fleshed, characterized by low carotenoid levels and by the presence of recessive chy2 alleles; and orange-fleshed, characterized by high levels of zeaxanthin but low levels of xanthophyll esters, and homozygosity for a Zeaxanthin Epoxidase (ZEP) recessive allele. Novel CHY2 and ZEP alleles were identified in the collection. Multivariate analysis identified several groups of co-regulated non-polar compounds, and resulted in the grouping of the genotypes according to flesh color, suggesting that extensive cross-talk exists between the carotenoid pathway and other metabolite pathways in tubers. Postharvest traits like tuber dormancy and weight loss during storage showed little correlation with tuber carotenoid content, with the exception of zeaxanthin and its esters. Other tuber metabolites, such as glucose, monogalactosyldiacyglycerol (a glycolipid), or suberin precursors, showed instead significant correlations with both traits.
Collapse
Affiliation(s)
- Maria Sulli
- ENEA, Casaccia Research Center, Via Anguillarese 301, Roma, Italy
- Scuola Superiore S. Anna, Piazza Martiri della Libertà 33, Pisa, Italy
| | - Giuseppe Mandolino
- CREA-Centro Cerealicoltura e Colture Industriali, Sede di Bologna, Via di Corticella 133, Bologna, Italy
| | - Monica Sturaro
- CREA- Centro Cerealicoltura e Colture Industriali, Sede di Bergamo, Via Stezzano 24, Bergamo, Italy
| | - Chiara Onofri
- CREA-Centro Cerealicoltura e Colture Industriali, Sede di Bologna, Via di Corticella 133, Bologna, Italy
| | | | - Bruno Parisi
- CREA-Centro Cerealicoltura e Colture Industriali, Sede di Bologna, Via di Corticella 133, Bologna, Italy
| | - Giovanni Giuliano
- ENEA, Casaccia Research Center, Via Anguillarese 301, Roma, Italy
- * E-mail:
| |
Collapse
|
18
|
RNA-Seq using bulked recombinant inbred line populations uncovers the importance of brassinosteroid for seed longevity after priming treatments. Sci Rep 2017; 7:8095. [PMID: 28808238 PMCID: PMC5556009 DOI: 10.1038/s41598-017-08116-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 07/03/2017] [Indexed: 11/22/2022] Open
Abstract
Seed priming is a commercially used technique for improving seed performance including germination. However, the treatment sometimes reduces seed longevity as a side effect, limiting the storable period or longevity of the seeds. To overcome this problem, molecular mechanisms involved in the loss of seed longevity during priming were analyzed using natural variations of Arabidopsis thaliana. We found that the Est-1 accession retained longevity for longer after priming compared to the reference accession Col-0. QTL analysis using 279 recombinant inbred lines (RILs) derived from the Est-1 × Col-0 detected three QTL regions associated with the loss of seed longevity during priming. Bulked transcriptome analysis (RNA-Seq with bulked RIL populations) revealed that genes related to brassinosteroid (BR) biosynthesis/signaling and cell wall modification were highly expressed in primed seeds with shorter longevity. After priming, BR-deficient mutants cyp85a1/a2 and det2 showed significantly longer longevity than the wild type (WT). Moreover, tetrazolium staining indicated that mutant seed coats were less permeable after priming than those of WT. We suggest that the loss of seed longevity in primed seed is due to increased seed coat permeability, which is positively regulated, at least partly, via BR signaling.
Collapse
|
19
|
Kumar J, Gupta DS, Gupta S, Dubey S, Gupta P, Kumar S. Quantitative trait loci from identification to exploitation for crop improvement. PLANT CELL REPORTS 2017; 36:1187-1213. [PMID: 28352970 DOI: 10.1007/s00299-017-2127-y] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 03/09/2017] [Indexed: 05/24/2023]
Abstract
Advancement in the field of genetics and genomics after the discovery of Mendel's laws of inheritance has led to map the genes controlling qualitative and quantitative traits in crop plant species. Mapping of genomic regions controlling the variation of quantitatively inherited traits has become routine after the advent of different types of molecular markers. Recently, the next generation sequencing methods have accelerated the research on QTL analysis. These efforts have led to the identification of more closely linked molecular markers with gene/QTLs and also identified markers even within gene/QTL controlling the trait of interest. Efforts have also been made towards cloning gene/QTLs or identification of potential candidate genes responsible for a trait. Further new concepts like crop QTLome and QTL prioritization have accelerated precise application of QTLs for genetic improvement of complex traits. In the past years, efforts have also been made in exploitation of a number of QTL for improving grain yield or other agronomic traits in various crops through markers assisted selection leading to cultivation of these improved varieties at farmers' field. In present article, we reviewed QTLs from their identification to exploitation in plant breeding programs and also reviewed that how improved cultivars developed through introgression of QTLs have improved the yield productivity in many crops.
Collapse
Affiliation(s)
- Jitendra Kumar
- Division of Crop Improvement, ICAR-Indian Institute of Pulses Research, Kanpur, India.
| | - Debjyoti Sen Gupta
- Division of Crop Improvement, ICAR-Indian Institute of Pulses Research, Kanpur, India
| | - Sunanda Gupta
- Division of Crop Improvement, ICAR-Indian Institute of Pulses Research, Kanpur, India
| | - Sonali Dubey
- Division of Crop Improvement, ICAR-Indian Institute of Pulses Research, Kanpur, India
| | - Priyanka Gupta
- Division of Crop Improvement, ICAR-Indian Institute of Pulses Research, Kanpur, India
| | - Shiv Kumar
- International Center for Agricultural Research in the Dry Areas (ICARDA), Rabat-Institutes, B.P. 6299, Rabat, Morocco
| |
Collapse
|
20
|
A Chromosome-Scale Assembly of the Bactrocera cucurbitae Genome Provides Insight to the Genetic Basis of white pupae. G3-GENES GENOMES GENETICS 2017; 7:1927-1940. [PMID: 28450369 PMCID: PMC5473769 DOI: 10.1534/g3.117.040170] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Genetic sexing strains (GSS) used in sterile insect technique (SIT) programs are textbook examples of how classical Mendelian genetics can be directly implemented in the management of agricultural insect pests. Although the foundation of traditionally developed GSS are single locus, autosomal recessive traits, their genetic basis are largely unknown. With the advent of modern genomic techniques, the genetic basis of sexing traits in GSS can now be further investigated. This study is the first of its kind to integrate traditional genetic techniques with emerging genomics to characterize a GSS using the tephritid fruit fly pest Bactrocera cucurbitae as a model. These techniques include whole-genome sequencing, the development of a mapping population and linkage map, and quantitative trait analysis. The experiment designed to map the genetic sexing trait in B. cucurbitae, white pupae (wp), also enabled the generation of a chromosome-scale genome assembly by integrating the linkage map with the assembly. Quantitative trait loci analysis revealed SNP loci near position 42 MB on chromosome 3 to be tightly linked to wp Gene annotation and synteny analysis show a near perfect relationship between chromosomes in B. cucurbitae and Muller elements A-E in Drosophila melanogaster This chromosome-scale genome assembly is complete, has high contiguity, was generated using a minimal input DNA, and will be used to further characterize the genetic mechanisms underlying wp Knowledge of the genetic basis of genetic sexing traits can be used to improve SIT in this species and expand it to other economically important Diptera.
Collapse
|
21
|
Chen L, Gao W, Chen S, Wang L, Zou J, Liu Y, Wang H, Chen Z, Guo T. High-resolution QTL mapping for grain appearance traits and co-localization of chalkiness-associated differentially expressed candidate genes in rice. RICE (NEW YORK, N.Y.) 2016; 9:48. [PMID: 27659284 PMCID: PMC5033801 DOI: 10.1186/s12284-016-0121-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 09/14/2016] [Indexed: 05/19/2023]
Abstract
BACKGROUND Grain appearance quality is a main determinant of market value in rice and one of the highly important traits requiring improvement in breeding programs. The genetic basis of grain shape and endosperm chalkiness have been given significant attention because of their importance in affecting grain quality. Meanwhile, the introduction of NGS (Next Generation Sequencing) has a significant part to play in the area of genomics, and offers the possibility for high-resolution genetic map construction, population genetics analysis and systematic expression profile study. RESULTS A RIL population derived from an inter-subspecific cross between indica rice PYZX and japonica rice P02428 was generated, based on the significant variations for the grain morphology and cytological structure between these two parents. Using the Genotyping-By-Sequencing (GBS) approach, 2711 recombination bin markers with an average physical length of 137.68 kb were obtained, and a high-density genetic map was constructed. Global genetic mapping of QTLs affecting grain shape and chalkiness traits was performed across four environments and the newly identified stable loci were obtained. Twelve important QTL clusters were detected, four of which were coincident with the genomic regions of cloned genes or fine mapped QTL reported. Eight novel QTL clusters (including six for grain shape, one for chalkiness, and one for both grain shape and chalkiness) were firstly obtained and highlighted the value and reliability of the QTL analysis. The important QTL cluster on chromosome 5 affects multiple traits including circularity (CS), grain width (GW), area size of grain (AS), percentage of grains with chalkiness (PGWC) and degree of endosperm chalkiness (DEC), indicating some potentially pleiotropic effects. The transcriptome analysis demonstrated an available gene expression profile responsible for the development of chalkiness, and several DEGs (differentially expressed genes) were co-located nearby the three chalkiness-related QTL regions on chromosomes 5, 7, and 8. Candidate genes were extrapolated, which were suitable for functional validation and breeding utilization. CONCLUSION QTLs affecting grain shape (grain width, grain length, length-width ratio, circularity, area size of grain, and perimeter length of grain) and chalkiness traits (percentage of grains with chalkiness and degree of endosperm chalkiness) were mapped with the high-density GBS-SNP based markers. The important differentially expressed genes (DEGs) were co-located in the QTL cluster regions on chromosomes 5, 7 and 8 affecting PGWC and DEC parameters. Our research provides a crucial insight into the genetic architecture of rice grain shape and chalkiness, and acquired potential candidate loci for molecular cloning and grain quality improvement.
Collapse
Affiliation(s)
- Likai Chen
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642, China
| | - Weiwei Gao
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642, China
| | - Siping Chen
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642, China
| | - Liping Wang
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642, China
| | - Jiyong Zou
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Agricultural Technology Extension, Guangzhou, 510520, China
| | - Yongzhu Liu
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642, China
| | - Hui Wang
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642, China
| | - Zhiqiang Chen
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642, China.
| | - Tao Guo
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642, China.
| |
Collapse
|
22
|
van Muijen D, Anithakumari AM, Maliepaard C, Visser RGF, van der Linden CG. Systems genetics reveals key genetic elements of drought induced gene regulation in diploid potato. PLANT, CELL & ENVIRONMENT 2016; 39:1895-1908. [PMID: 27353051 DOI: 10.1111/pce.12744] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Revised: 03/01/2016] [Accepted: 03/03/2016] [Indexed: 06/06/2023]
Abstract
In plants, tolerance to drought stress is a result of numerous minor effect loci in which transcriptional regulation contributes significantly to the observed phenotypes. Under severe drought conditions, a major expression quantitative trait loci hotspot was identified on chromosome five in potato. A putative Nuclear factor y subunit C4 was identified as key candidate in the regulatory cascade in response to drought. Further investigation of the eQTL hotspots suggests a role for a putative Homeobox leucine zipper protein 12 in relation to drought in potato. Genes strongly co-expressed with Homeobox leucine zipper protein 12 were plant growth regulators responsive to water deficit stress in Arabidopsis thaliana, implying a possible conserved mechanism. Integrative analysis of genetic, genomic, phenotypic and transcriptomic data provided insights in the downstream functional components of the drought response. The abscisic acid- and environmental stress-inducible protein TAS14 was highly induced by severe drought in potato and acts as a reliable biomarker for the level of stress perceived by the plant. The systems genetics approach supported a role for multiple genes responsive to severe drought stress of Solanum tuberosum. The combination of gene regulatory networks, expression quantitative trait loci mapping and phenotypic analysis proved useful for candidate gene selection.
Collapse
Affiliation(s)
- Dennis van Muijen
- Wageningen UR Plant Breeding, Wageningen University and Research Centre, P.O. Box 386, 6700 AJ, Wageningen, The Netherlands
- Graduate School Experimental Plant Sciences (EPS), The Netherlands
| | - A M Anithakumari
- Wageningen UR Plant Breeding, Wageningen University and Research Centre, P.O. Box 386, 6700 AJ, Wageningen, The Netherlands
- Graduate School Experimental Plant Sciences (EPS), The Netherlands
| | - Chris Maliepaard
- Wageningen UR Plant Breeding, Wageningen University and Research Centre, P.O. Box 386, 6700 AJ, Wageningen, The Netherlands
- Graduate School Experimental Plant Sciences (EPS), The Netherlands
| | - Richard G F Visser
- Wageningen UR Plant Breeding, Wageningen University and Research Centre, P.O. Box 386, 6700 AJ, Wageningen, The Netherlands
- Graduate School Experimental Plant Sciences (EPS), The Netherlands
| | - C Gerard van der Linden
- Wageningen UR Plant Breeding, Wageningen University and Research Centre, P.O. Box 386, 6700 AJ, Wageningen, The Netherlands
- Graduate School Experimental Plant Sciences (EPS), The Netherlands
| |
Collapse
|
23
|
Acharjee A, Kloosterman B, Visser RGF, Maliepaard C. Integration of multi-omics data for prediction of phenotypic traits using random forest. BMC Bioinformatics 2016; 17 Suppl 5:180. [PMID: 27295212 PMCID: PMC4905610 DOI: 10.1186/s12859-016-1043-4] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Background In order to find genetic and metabolic pathways related to phenotypic traits of interest, we analyzed gene expression data, metabolite data obtained with GC-MS and LC-MS, proteomics data and a selected set of tuber quality phenotypic data from a diploid segregating mapping population of potato. In this study we present an approach to integrate these ~ omics data sets for the purpose of predicting phenotypic traits. This gives us networks of relatively small sets of interrelated ~ omics variables that can predict, with higher accuracy, a quality trait of interest. Results We used Random Forest regression for integrating multiple ~ omics data for prediction of four quality traits of potato: tuber flesh colour, DSC onset, tuber shape and enzymatic discoloration. For tuber flesh colour beta-carotene hydroxylase and zeaxanthin epoxidase were ranked first and forty-fourth respectively both of which have previously been associated with flesh colour in potato tubers. Combining all the significant genes, LC-peaks, GC-peaks and proteins, the variation explained was 75 %, only slightly more than what gene expression or LC-MS data explain by themselves which indicates that there are correlations among the variables across data sets. For tuber shape regressed on the gene expression, LC-MS, GC-MS and proteomics data sets separately, only gene expression data was found to explain significant variation. For DSC onset, we found 12 significant gene expression, 5 metabolite levels (GC) and 2 proteins that are associated with the trait. Using those 19 significant variables, the variation explained was 45 %. Expression QTL (eQTL) analyses showed many associations with genomic regions in chromosome 2 with also the highest explained variation compared to other chromosomes. Transcriptomics and metabolomics analysis on enzymatic discoloration after 5 min resulted in 420 significant genes and 8 significant LC metabolites, among which two were putatively identified as caffeoylquinic acid methyl ester and tyrosine. Conclusions In this study, we made a strategy for selecting and integrating multiple ~ omics data using random forest method and selected representative individual peaks for networks based on eQTL, mQTL or pQTL information. Network analysis was done to interpret how a particular trait is associated with gene expression, metabolite and protein data. Electronic supplementary material The online version of this article (doi:10.1186/s12859-016-1043-4) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Animesh Acharjee
- Wageningen UR Plant Breeding, Wageningen University & Research Centre, PO Box 6700 AJ, Wageningen, The Netherlands.,MRC Human Nutrition Research, 120 Fulbourn Road, Cambridge, CB1 9NL, UK
| | - Bjorn Kloosterman
- Wageningen UR Plant Breeding, Wageningen University & Research Centre, PO Box 6700 AJ, Wageningen, The Netherlands.,Keygene NV, PO Box 216, 6700 AE, Wageningen, The Netherlands
| | - Richard G F Visser
- Wageningen UR Plant Breeding, Wageningen University & Research Centre, PO Box 6700 AJ, Wageningen, The Netherlands
| | - Chris Maliepaard
- Wageningen UR Plant Breeding, Wageningen University & Research Centre, PO Box 6700 AJ, Wageningen, The Netherlands.
| |
Collapse
|
24
|
Assessment of Functional EST-SSR Markers (Sugarcane) in Cross-Species Transferability, Genetic Diversity among Poaceae Plants, and Bulk Segregation Analysis. GENETICS RESEARCH INTERNATIONAL 2016; 2016:7052323. [PMID: 27340568 PMCID: PMC4908241 DOI: 10.1155/2016/7052323] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Revised: 04/13/2016] [Accepted: 04/26/2016] [Indexed: 11/17/2022]
Abstract
Expressed sequence tags (ESTs) are important resource for gene discovery, gene expression and its regulation, molecular marker development, and comparative genomics. We procured 10000 ESTs and analyzed 267 EST-SSRs markers through computational approach. The average density was one SSR/10.45 kb or 6.4% frequency, wherein trinucleotide repeats (66.74%) were the most abundant followed by di- (26.10%), tetra- (4.67%), penta- (1.5%), and hexanucleotide (1.2%) repeats. Functional annotations were done and after-effect newly developed 63 EST-SSRs were used for cross transferability, genetic diversity, and bulk segregation analysis (BSA). Out of 63 EST-SSRs, 42 markers were identified owing to their expansion genetics across 20 different plants which amplified 519 alleles at 180 loci with an average of 2.88 alleles/locus and the polymorphic information content (PIC) ranged from 0.51 to 0.93 with an average of 0.83. The cross transferability ranged from 25% for wheat to 97.22% for Schlerostachya, with an average of 55.86%, and genetic relationships were established based on diversification among them. Moreover, 10 EST-SSRs were recognized as important markers between bulks of pooled DNA of sugarcane cultivars through BSA. This study highlights the employability of the markers in transferability, genetic diversity in grass species, and distinguished sugarcane bulks.
Collapse
|
25
|
Abstract
Plastids are ubiquitously present in plants and are the organelles for carotenoid biosynthesis and storage. Based on their morphology and function, plastids are classified into various types, i.e. proplastids, etioplasts, chloroplasts, amyloplasts, and chromoplasts. All plastids, except proplastids, can synthesize carotenoids. However, plastid types have a profound effect on carotenoid accumulation and stability. In this chapter, we discuss carotenoid biosynthesis and regulation in various plastids with a focus on carotenoids in chromoplasts. Plastid transition related to carotenoid biosynthesis and the different capacity of various plastids to sequester carotenoids and the associated effect on carotenoid stability are described in light of carotenoid accumulation in plants.
Collapse
Affiliation(s)
- Li Li
- Robert W. Holley Center for Agriculture and Health, USDA-ARS, Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA.
| | - Hui Yuan
- Robert W. Holley Center for Agriculture and Health, USDA-ARS, Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | - Yunliu Zeng
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, China
| | - Qiang Xu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, China
| |
Collapse
|
26
|
Muktar MS, Lübeck J, Strahwald J, Gebhardt C. Selection and validation of potato candidate genes for maturity corrected resistance to Phytophthora infestans based on differential expression combined with SNP association and linkage mapping. Front Genet 2015; 6:294. [PMID: 26442110 PMCID: PMC4585299 DOI: 10.3389/fgene.2015.00294] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Accepted: 09/04/2015] [Indexed: 12/23/2022] Open
Abstract
Late blight of potato (Solanum tuberosum L.) caused by the oomycete Phytophthora infestans (Mont.) de Bary, is one of the most important bottlenecks of potato production worldwide. Cultivars with high levels of durable, race unspecific, quantitative resistance are part of a solution to this problem. However, breeding for quantitative resistance is hampered by the correlation between resistance and late plant maturity, which is an undesirable agricultural attribute. The objectives of our research are (i) the identification of genes that condition quantitative resistance to P. infestans not compromised by late plant maturity and (ii) the discovery of diagnostic single nucleotide polymorphism (SNP) markers to be used as molecular tools to increase efficiency and precision of resistance breeding. Twenty two novel candidate genes were selected based on comparative transcript profiling by SuperSAGE (serial analysis of gene expression) in groups of plants with contrasting levels of maturity corrected resistance (MCR). Reproducibility of differential expression was tested by quantitative real time PCR and allele specific pyrosequencing in four new sets of genotype pools with contrasting late blight resistance levels, at three infection time points and in three independent infection experiments. Reproducibility of expression patterns ranged from 28 to 97%. Association mapping in a panel of 184 tetraploid cultivars identified SNPs in five candidate genes that were associated with MCR. These SNPs can be used in marker-assisted resistance breeding. Linkage mapping in two half-sib families (n = 111) identified SNPs in three candidate genes that were linked with MCR. The differentially expressed genes that showed association and/or linkage with MCR putatively function in phytosterol synthesis, fatty acid synthesis, asparagine synthesis, chlorophyll synthesis, cell wall modification, and in the response to pathogen elicitors.
Collapse
Affiliation(s)
- Meki S Muktar
- Department for Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research Cologne, Germany
| | - Jens Lübeck
- Saka-Pflanzenzucht GmbH & Co. KG Windeby, Germany
| | | | - Christiane Gebhardt
- Department for Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research Cologne, Germany
| |
Collapse
|
27
|
Malacarne G, Costantini L, Coller E, Battilana J, Velasco R, Vrhovsek U, Grando MS, Moser C. Regulation of flavonol content and composition in (Syrah×Pinot Noir) mature grapes: integration of transcriptional profiling and metabolic quantitative trait locus analyses. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:4441-53. [PMID: 26071529 PMCID: PMC4507773 DOI: 10.1093/jxb/erv243] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Flavonols are a ubiquitous class of flavonoids that accumulate preferentially in flowers and mature berries. Besides their photo-protective function, they play a fundamental role during winemaking, stabilizing the colour by co-pigmentation with anthocyanins and contributing to organoleptic characteristics. Although the general flavonol pathway has been genetically and biochemically elucidated, the genetic control of flavonol content and composition at harvest is still not clear. To this purpose, the grapes of 170 segregating F1 individuals from a 'Syrah'×'Pinot Noir' population were evaluated at the mature stage for the content of six flavonol aglycons in four seasons. Metabolic data in combination with genetic data enabled the identification of 16 mQTLs (metabolic quantitative trait loci). For the first time, major genetic control by the linkage group 2 (LG 2)/MYBA region on flavonol variation, in particular of tri-hydroxylated flavonols, is demonstrated. Moreover, seven regions specifically associated with the fine control of flavonol biosynthesis are identified. Gene expression profiling of two groups of individuals significantly divergent for their skin flavonol content identified a large set of differentially modulated transcripts. Among these, the transcripts coding for MYB and bZIP transcription factors, methyltranferases, and glucosyltranferases specific for flavonols, proteins, and factors belonging to the UV-B signalling pathway and co-localizing with the QTL regions are proposed as candidate genes for the fine regulation of flavonol content and composition in mature grapes.
Collapse
Affiliation(s)
- Giulia Malacarne
- Genomics and Biology of Fruit Crops Department, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010 S. Michele all'Adige, Trento, Italy
| | - Laura Costantini
- Genomics and Biology of Fruit Crops Department, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010 S. Michele all'Adige, Trento, Italy
| | - Emanuela Coller
- Computational Biology Department, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010 S. Michele all'Adige, Trento, Italy
| | - Juri Battilana
- Genomics and Biology of Fruit Crops Department, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010 S. Michele all'Adige, Trento, Italy
| | - Riccardo Velasco
- Genomics and Biology of Fruit Crops Department, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010 S. Michele all'Adige, Trento, Italy
| | - Urska Vrhovsek
- Food Quality and Nutrition Department, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010 S. Michele all'Adige, Trento, Italy
| | - Maria Stella Grando
- Genomics and Biology of Fruit Crops Department, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010 S. Michele all'Adige, Trento, Italy
| | - Claudio Moser
- Genomics and Biology of Fruit Crops Department, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010 S. Michele all'Adige, Trento, Italy
| |
Collapse
|
28
|
Bajaj D, Saxena MS, Kujur A, Das S, Badoni S, Tripathi S, Upadhyaya HD, Gowda CLL, Sharma S, Singh S, Tyagi AK, Parida SK. Genome-wide conserved non-coding microsatellite (CNMS) marker-based integrative genetical genomics for quantitative dissection of seed weight in chickpea. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:1271-90. [PMID: 25504138 PMCID: PMC4339591 DOI: 10.1093/jxb/eru478] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Phylogenetic footprinting identified 666 genome-wide paralogous and orthologous CNMS (conserved non-coding microsatellite) markers from 5'-untranslated and regulatory regions (URRs) of 603 protein-coding chickpea genes. The (CT)n and (GA)n CNMS carrying CTRMCAMV35S and GAGA8BKN3 regulatory elements, respectively, are abundant in the chickpea genome. The mapped genic CNMS markers with robust amplification efficiencies (94.7%) detected higher intraspecific polymorphic potential (37.6%) among genotypes, implying their immense utility in chickpea breeding and genetic analyses. Seventeen differentially expressed CNMS marker-associated genes showing strong preferential and seed tissue/developmental stage-specific expression in contrasting genotypes were selected to narrow down the gene targets underlying seed weight quantitative trait loci (QTLs)/eQTLs (expression QTLs) through integrative genetical genomics. The integration of transcript profiling with seed weight QTL/eQTL mapping, molecular haplotyping, and association analyses identified potential molecular tags (GAGA8BKN3 and RAV1AAT regulatory elements and alleles/haplotypes) in the LOB-domain-containing protein- and KANADI protein-encoding transcription factor genes controlling the cis-regulated expression for seed weight in the chickpea. This emphasizes the potential of CNMS marker-based integrative genetical genomics for the quantitative genetic dissection of complex seed weight in chickpea.
Collapse
Affiliation(s)
- Deepak Bajaj
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Maneesha S Saxena
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Alice Kujur
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Shouvik Das
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Saurabh Badoni
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Shailesh Tripathi
- Division of Genetics, Indian Agricultural Research Institute (IARI), New Delhi 110012, India
| | - Hari D Upadhyaya
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502324, Telangana, India
| | - C L L Gowda
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502324, Telangana, India
| | - Shivali Sharma
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502324, Telangana, India
| | - Sube Singh
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502324, Telangana, India
| | - Akhilesh K Tyagi
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Swarup K Parida
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| |
Collapse
|
29
|
Liu WY, Kang JH, Jeong HS, Choi HJ, Yang HB, Kim KT, Choi D, Choi GJ, Jahn M, Kang BC. Combined use of bulked segregant analysis and microarrays reveals SNP markers pinpointing a major QTL for resistance to Phytophthora capsici in pepper. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2014; 127:2503-13. [PMID: 25208646 DOI: 10.1007/s00122-014-2394-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2014] [Accepted: 08/28/2014] [Indexed: 05/03/2023]
Abstract
Bulked segregant analysis (BSA) using Affymetrix GeneChips revealed candidate genes underlying the major QTL for Phytophthora capsici resistance in Capsicum. Using the candidate genes, reliable markers for Phytophthora resistance were developed and validated. Phytophthora capsici L. is one of the most destructive pathogens of pepper (Capsicum spp.). Resistance of pepper against P. capsici is controlled by quantitative trait loci (QTL), including a major QTL on chromosome 5 that is the predominant contributor to resistance. Here, to maximize the effect of this QTL and study its underlying genes, an F2 population and recombinant inbred lines were inoculated with P. capsici strain JHAI1-7 zoospores at a low concentration (3 × 10(3)/mL). Resistance phenotype segregation ratios for the populations fit a 3:1 and 1:1 (resistant:susceptible) segregation model, respectively, consistent with a single dominant gene model. Bulked segregant analysis (BSA) using Affymetrix GeneChips revealed a single position polymorphism (SPP) marker mapping to the major QTL. When this SPP marker (Phyto5SAR) together with other SNP markers located on chromosome 5 was used to confirm the position of the major QTL, Phyto5SAR showed the highest LOD value at the QTL. A scaffold sequence (scaffold194) containing Phyto5SAR was identified from the C. annuum genome database. The scaffold contained two putative NBS-LRR genes and one SAR 8.2A gene as candidates for contributing to P. capsici resistance. Markers linked to these genes were developed and validated by testing 100 F1 commercial cultivars. Among the markers, Phyto5NBS1 showed about 90% accuracy in predicting resistance phenotypes to a low-virulence P. capsici isolate. These results suggest that Phyto5NBS1 is a reliable marker for P. capsici resistance and can be used for identification of a gene(s) underlying the major QTL on chromosome 5.
Collapse
Affiliation(s)
- Wing-Yee Liu
- Department of Plant Science, Plant Genomics and Breeding Institute and Research Institute for Agriculture and Life Sciences, Seoul National University, 1 Gwanak-ro Gwank-gu, 151-921, Seoul, Republic of Korea
| | | | | | | | | | | | | | | | | | | |
Collapse
|
30
|
Campbell R, Pont SDA, Morris JA, McKenzie G, Sharma SK, Hedley PE, Ramsay G, Bryan GJ, Taylor MA. Genome-wide QTL and bulked transcriptomic analysis reveals new candidate genes for the control of tuber carotenoid content in potato (Solanum tuberosum L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2014; 127:1917-33. [PMID: 24965888 DOI: 10.1007/s00122-014-2349-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2014] [Accepted: 06/07/2014] [Indexed: 05/05/2023]
Abstract
Genome-wide QTL analysis of potato tuber carotenoid content was investigated in populations of Solanum tuberosum Group Phureja that segregate for flesh colour, revealing a novel major QTL on chromosome 9. The carotenoid content of edible plant storage organs is a key nutritional and quality trait. Although the structural genes that encode the biosynthetic enzymes are well characterised, much less is known about the factors that determine overall storage organ content. In this study, genome-wide QTL mapping, in concert with an efficient 'genetical genomics' analysis using bulked samples, has been employed to investigate the genetic architecture of potato tuber carotenoid content. Two diploid populations of Solanum tuberosum Group Phureja were genotyped (AFLP, SSR and DArT markers) and analysed for their tuber carotenoid content over two growing seasons. Common to both populations were QTL that explained relatively small proportions of the variation in constituent carotenoids and a major QTL on chromosome 3 explaining up to 71 % of the variation in carotenoid content. In one of the populations (01H15), a second major carotenoid QTL was identified on chromosome 9, explaining up to 20 % of the phenotypic variation. Whereas the major chromosome 3 QTL was likely to be due to an allele of a gene encoding β-carotene hydroxylase, no known carotenoid biosynthetic genes are located in the vicinity of the chromosome 9 QTL. A unique expression profiling strategy using phenotypically distinct bulks comprised individuals with similar carotenoid content provided further support for the QTL mapping to chromosome 9. This study shows the potential of using the potato genome sequence to link genetic maps to data arising from eQTL approaches to enhance the discovery of candidate genes underlying QTLs.
Collapse
Affiliation(s)
- Raymond Campbell
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | | | | | | | | | | | | | | | | |
Collapse
|
31
|
D'hoop BB, Keizer PLC, Paulo MJ, Visser RGF, van Eeuwijk FA, van Eck HJ. Identification of agronomically important QTL in tetraploid potato cultivars using a marker-trait association analysis. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2014; 127:731-48. [PMID: 24408376 DOI: 10.1007/s00122-013-2254-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2013] [Accepted: 12/13/2013] [Indexed: 05/23/2023]
Abstract
Nineteen tuber quality traits in potato were phenotyped in 205 cultivars and 299 breeder clones. Association analysis using 3364 AFLP loci and 653 SSR-alleles identified QTL for these traits. Two association mapping panels were analysed for marker-trait associations to identify quantitative trait loci (QTL). The first panel comprised 205 historical and contemporary tetraploid potato cultivars that were phenotyped in field trials at two locations with two replicates (the academic panel). The second panel consisted of 299 potato cultivars and included recent breeds obtained from five Dutch potato breeding companies and reference cultivars (the industrial panel). Phenotypic data for the second panel were collected during subsequent clonal selection generations at the individual breeding companies. QTL were identified for 19 agro-morphological and quality traits. Two association mapping models were used: a baseline model without, and a more advanced model with correction for population structure and genetic relatedness. Correction for population structure and genetic relatedness was performed with a kinship matrix estimated from marker information. The detected QTL partly not only confirmed previous studies, e.g. for tuber shape and frying colour, but also new QTL were found like for after baking darkening and enzymatic browning. Pleiotropic effects could be discerned for several QTL.
Collapse
Affiliation(s)
- Björn B D'hoop
- Plant Breeding, Wageningen University and Research Centre, P.O. Box 386, 6700 AJ, Wageningen, The Netherlands
| | | | | | | | | | | |
Collapse
|
32
|
Neubauer JD, Lulai EC, Thompson AL, Suttle JC, Bolton MD, Campbell LG. Molecular and cytological aspects of native periderm maturation in potato tubers. JOURNAL OF PLANT PHYSIOLOGY 2013; 170:413-423. [PMID: 23246026 DOI: 10.1016/j.jplph.2012.10.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2012] [Revised: 10/30/2012] [Accepted: 10/31/2012] [Indexed: 06/01/2023]
Abstract
Mature native periderm that exhibits resistance to excoriation (RE) is the primary defense for potato tubers against abiotic and biotic challenges. However, little is known about the physiology of periderm maturation and associated gene expressions. In this study, periderm maturation events and associated gene expressions were determined in tubers of two diverse potato genotypes (NDTX4271-5R (ND) and Russet Burbank (RB); 2008 and 2009 crops) at four harvest maturities ranging from immature (non-senesced vines and low RE) to mature (senesced vines and high RE). Approximately 104 d after planting, the fine balance of accumulation and loss of periderm phellem cell layers showed signs of subsiding, indicating cessation of cell division by the phellogen. Phellogen radial cell walls thickened as periderm matured throughout the harvests, increasing RE/skin-set. In both genotypes, the cell cycle gene cyclin-dependent kinase B (StCDKB) rapidly down-regulated after the second harvest coinciding with apparent cessation of cell division. Expression patterns of genes encoding epidermal growth factor binding protein (StEBP) and cyclin-dependent kinase regulatory subunit (StCKS1At) were less indicative of phellogen inactivation and periderm maturation. Genes encoding the structural cell wall proteins extensin (StExt1) for ND and extensin-like (StExtlk) for ND and RB remained up-regulated respectively by the second harvest, suggesting involvement with completion of phellem cell accumulation and on-set of periderm maturation. The expression of genes encoding pectin methyl esterase (StPME), StExt1 and a cell wall strengthening "tyrosine-and lysine-rich protein" (StTLRP) increased in phellogen cells from later harvests of ND tubers, but were down regulated in RB tubers; this suggests roles in phellem cell generation and completion of delayed cell wall development in non-meristematic phellogen cells of ND, a red skinned phenotype. StCDKB and StPrePME genes were rapidly down-regulated by the third harvest for both genotypes. Collectively, these results suggest that down-regulation of these genes coordinates with on-set of periderm maturation and skin-set progression.
Collapse
Affiliation(s)
- Jonathan D Neubauer
- United States Department of Agriculture, Agricultural Research Service, Sugarbeet and Potato Unit, Northern Crop Science Laboratory, Fargo, ND 58102-2765, United States
| | | | | | | | | | | |
Collapse
|
33
|
Sherman A, Eshed R, Harel-Beja R, Tzuri G, Portnoy V, Cohen S, Rubinstein M, Schaffer AA, Burger J, Katzir N, Ophir R. Combining bulk segregation analysis and microarrays for mapping of the pH trait in melon. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2013; 126:349-358. [PMID: 23070028 DOI: 10.1007/s00122-012-1983-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2012] [Accepted: 09/15/2012] [Indexed: 06/01/2023]
Abstract
The availability of sequence information for many plants has opened the way to advanced genetic analysis in many non-model plants. Nevertheless, exploration of genetic variation on a large scale and its use as a tool for the identification of traits of interest are still rare. In this study, we combined a bulk segregation approach with our own-designed microarrays to map the pH locus that influences fruit pH in melon. Using these technologies, we identified a set of markers that are genetically linked to the pH trait. Further analysis using a set of melon cultivars demonstrated that some of these markers are tightly linked to the pH trait throughout our germplasm collection. These results validate the utility of combining microarray technology with a bulk segregation approach in mapping traits of interest in non-model plants.
Collapse
Affiliation(s)
- Amir Sherman
- Genomic Unit, Institute of Plant Sciences, Volcani Research Center, Agricultural Research Organization, 50250 Bet Dagan, Israel.
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
34
|
Crops that feed the world 8: Potato: are the trends of increased global production sustainable? Food Secur 2012. [DOI: 10.1007/s12571-012-0220-1] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
|
35
|
Sun M, Hua W, Liu J, Huang S, Wang X, Liu G, Wang H. Design of new genome- and gene-sourced primers and identification of QTL for seed oil content in a specially high-oil Brassica napus cultivar. PLoS One 2012; 7:e47037. [PMID: 23077542 PMCID: PMC3470593 DOI: 10.1371/journal.pone.0047037] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2012] [Accepted: 09/10/2012] [Indexed: 11/18/2022] Open
Abstract
Rapeseed (Brassica napus L.) is one of most important oilseed crops in the world. There are now various rapeseed cultivars in nature that differ in their seed oil content because they vary in oil-content alleles and there are high-oil alleles among the high-oil rapeseed cultivars. For these experiments, we generated doubled haploid (DH) lines derived from the cross between the specially high-oil cultivar zy036 whose seed oil content is approximately 50% and the specially low-oil cultivar 51070 whose seed oil content is approximately 36%. First, to address the deficiency in polymorphic markers, we designed 5944 pairs of newly developed genome-sourced primers and 443 pairs of newly developed primers related to oil-content genes to complement the 2244 pairs of publicly available primers. Second, we constructed a new DH genetic linkage map using 527 molecular markers, consisting of 181 publicly available markers, 298 newly developed genome-sourced markers and 48 newly developed markers related to oil-content genes. The map contained 19 linkage groups, covering a total length of 2,265.54 cM with an average distance between markers of 4.30 cM. Third, we identified quantitative trait loci (QTL) for seed oil content using field data collected at three sites over 3 years, and found a total of 12 QTL. Of the 12 QTL associated with seed oil content identified, 9 were high-oil QTL which derived from the specially high-oil cultivar zy036. Two high-oil QTL on chromosomes A2 and C9 co-localized in two out of three trials. By QTL mapping for seed oil content, we found four candidate genes for seed oil content related to four gene markers: GSNP39, GSSR161, GIFLP106 and GIFLP046. This information will be useful for cloning functional genes correlated with seed oil content in the future.
Collapse
Affiliation(s)
- Meiyu Sun
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, People's Republic of China
| | - Wei Hua
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, People's Republic of China
| | - Jing Liu
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, People's Republic of China
| | - Shunmou Huang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, People's Republic of China
| | - Xinfa Wang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, People's Republic of China
| | - Guihua Liu
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, People's Republic of China
| | - Hanzhong Wang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, People's Republic of China
- * E-mail:
| |
Collapse
|
36
|
Kullan ARK, van Dyk MM, Hefer CA, Jones N, Kanzler A, Myburg AA. Genetic dissection of growth, wood basic density and gene expression in interspecific backcrosses of Eucalyptus grandis and E. urophylla. BMC Genet 2012; 13:60. [PMID: 22817272 PMCID: PMC3416674 DOI: 10.1186/1471-2156-13-60] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2012] [Accepted: 07/20/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND F1 hybrid clones of Eucalyptus grandis and E. urophylla are widely grown for pulp and paper production in tropical and subtropical regions. Volume growth and wood quality are priority objectives in Eucalyptus tree improvement. The molecular basis of quantitative variation and trait expression in eucalypt hybrids, however, remains largely unknown. The recent availability of a draft genome sequence (http://www.phytozome.net) and genome-wide genotyping platforms, combined with high levels of genetic variation and high linkage disequilibrium in hybrid crosses, greatly facilitate the detection of quantitative trait loci (QTLs) as well as underlying candidate genes for growth and wood property traits. In this study, we used Diversity Arrays Technology markers to assess the genetic architecture of volume growth (diameter at breast height, DBH) and wood basic density in four-year-old progeny of an interspecific backcross pedigree of E. grandis and E. urophylla. In addition, we used Illumina RNA-Seq expression profiling in the E. urophylla backcross family to identify cis- and trans-acting polymorphisms (eQTLs) affecting transcript abundance of genes underlying QTLs for wood basic density. RESULTS A total of five QTLs for DBH and 12 for wood basic density were identified in the two backcross families. Individual QTLs for DBH and wood basic density explained 3.1 to 12.2% of phenotypic variation. Candidate genes underlying QTLs for wood basic density on linkage groups 8 and 9 were found to share trans-acting eQTLs located on linkage groups 4 and 10, which in turn coincided with QTLs for wood basic density suggesting that these QTLs represent segregating components of an underlying transcriptional network. CONCLUSION This is the first demonstration of the use of next-generation expression profiling to quantify transcript abundance in a segregating tree population and identify candidate genes potentially affecting wood property variation. The QTLs identified in this study provide a resource for identifying candidate genes and developing molecular markers for marker-assisted breeding of volume growth and wood basic density. Our results suggest that integrated analysis of transcript and trait variation in eucalypt hybrids can be used to dissect the molecular basis of quantitative variation in wood property traits.
Collapse
Affiliation(s)
- Anand Raj Kumar Kullan
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0002, South Africa
| | | | | | | | | | | |
Collapse
|
37
|
Lu FH, Kwon SW, Yoon MY, Kim KT, Cho MC, Yoon MK, Park YJ. SNP marker integration and QTL analysis of 12 agronomic and morphological traits in F₈ RILs of pepper (Capsicum annuum L.). Mol Cells 2012; 34:25-34. [PMID: 22684870 PMCID: PMC3887781 DOI: 10.1007/s10059-012-0018-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2011] [Revised: 05/02/2012] [Accepted: 05/03/2012] [Indexed: 01/05/2023] Open
Abstract
Red pepper, Capsicum annuum L., has been attracting geneticists' and breeders' attention as one of the important agronomic crops. This study was to integrate 41 SNP markers newly developed from comparative transcriptomes into a previous linkage map, and map 12 agronomic and morphological traits into the integrated map. A total of 39 markers found precise position and were assigned to 13 linkage groups (LGs) as well as the unassigned LGe, leading to total 458 molecular markers present in this genetic map. Linkage mapping was supported by the physical mapping to tomato and potato genomes using BLAST retrieving, revealing at least two-thirds of the markers mapped to the corresponding LGs. A sum of 23 quantitative trait loci from 11 traits was detected using the composite interval mapping algorithm. A consistent interval between a035_1 and a170_1 on LG5 was detected as a main-effect locus among the resistance QTLs to Phytophthora capsici at high-, intermediate- and low-level tests, and interactions between the QTLs for high-level resistance test were found. Considering the epistatic effect, those QTLs could explain up to 98.25% of the phenotype variations of resistance. Moreover, 17 QTLs for another eight traits were found to locate on LG3, 4, and 12 mostly with varying phenotypic contribution. Furthermore, the locus for corolla color was mapped to LG10 as a marker. The integrated map and the QTLs identified would be helpful for current genetics research and crop breeding, especially in the Solanaceae family.
Collapse
Affiliation(s)
- Fu-Hao Lu
- Department of Plant Resources, College of Industrial Sciences, Kongju National University, Yesan 340-702,
Korea
| | - Soon-Wook Kwon
- Department of Plant Resources, College of Industrial Sciences, Kongju National University, Yesan 340-702,
Korea
- Legume Bio-Resource Center of Green Manure (LBRCGM), Kongju National University, Yesan 340-702,
Korea
| | - Min-Young Yoon
- Department of Plant Resources, College of Industrial Sciences, Kongju National University, Yesan 340-702,
Korea
| | - Ki-Taek Kim
- The Foundation of Agricultural Technology Commercialization and Transfer, Suwon 441-100,
Korea
| | - Myeong-Cheoul Cho
- Vegetable Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Suwon 441-440,
Korea
| | - Moo-Kyung Yoon
- Vegetable Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Suwon 441-440,
Korea
| | - Yong-Jin Park
- Department of Plant Resources, College of Industrial Sciences, Kongju National University, Yesan 340-702,
Korea
- Legume Bio-Resource Center of Green Manure (LBRCGM), Kongju National University, Yesan 340-702,
Korea
| |
Collapse
|
38
|
Neubauer JD, Lulai EC, Thompson AL, Suttle JC, Bolton MD. Wounding coordinately induces cell wall protein, cell cycle and pectin methyl esterase genes involved in tuber closing layer and wound periderm development. JOURNAL OF PLANT PHYSIOLOGY 2012; 169:586-595. [PMID: 22251796 DOI: 10.1016/j.jplph.2011.12.010] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2011] [Revised: 12/16/2011] [Accepted: 12/16/2011] [Indexed: 05/31/2023]
Abstract
Little is known about the coordinate induction of genes that may be involved in agriculturally important wound-healing events. In this study, wound-healing events were determined together with wound-induced expression profiles of selected cell cycle, cell wall protein, and pectin methyl esterase genes using two diverse potato genotypes and two harvests (NDTX4271-5R and Russet Burbank tubers; 2008 and 2009 harvests). By 5 d after wounding, the closing layer and a nascent phellogen had formed. Phellogen cell divisions generated phellem layers until cessation of cell division at 28 d after wounding for both genotypes and harvests. Cell cycle genes encoding epidermal growth factor binding protein (StEBP), cyclin-dependent kinase B (StCDKB) and cyclin-dependent kinase regulatory subunit (StCKS1At) were induced by 1 d after wounding; these expressions coordinated with related phellogen formation and the induction and cessation of phellem cell formation. Genes encoding the structural cell wall proteins extensin (StExt1) and extensin-like (StExtlk) were dramatically up-regulated by 1-5 d after wounding, suggesting involvement with closing layer and later phellem cell layer formation. Wounding up-regulated pectin methyl esterase genes (StPME and StPrePME); StPME expression increased during closing layer and phellem cell formation, whereas maximum expression of StPrePME occurred at 5-14 d after wounding, implicating involvement in later modifications for closing layer and phellem cell formation. The coordinate induction and expression profile of StTLRP, a gene encoding a cell wall strengthening "tyrosine-and lysine-rich protein," suggested a role in the formation of the closing layer followed by phellem cell generation and maturation. Collectively, the genes monitored were wound-inducible and their expression profiles markedly coordinated with closing layer formation and the index for phellogen layer meristematic activity during wound periderm development; results were more influenced by harvest than genotype. Importantly, StTLRP was the only gene examined that may be involved in phellogen cell wall thickening after cessation of phellogen cell division.
Collapse
Affiliation(s)
- Jonathan D Neubauer
- United States Department of Agriculture, Agricultural Research Service, Sugarbeet and Potato Unit, Northern Crop Science Laboratory, Fargo, ND 58102-2765, United States
| | | | | | | | | |
Collapse
|
39
|
Carreno-Quintero N, Acharjee A, Maliepaard C, Bachem CW, Mumm R, Bouwmeester H, Visser RG, Keurentjes JJ. Untargeted metabolic quantitative trait loci analyses reveal a relationship between primary metabolism and potato tuber quality. PLANT PHYSIOLOGY 2012; 158:1306-18. [PMID: 22223596 PMCID: PMC3291263 DOI: 10.1104/pp.111.188441] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2011] [Accepted: 12/26/2011] [Indexed: 05/18/2023]
Abstract
Recent advances in -omics technologies such as transcriptomics, metabolomics, and proteomics along with genotypic profiling have permitted dissection of the genetics of complex traits represented by molecular phenotypes in nonmodel species. To identify the genetic factors underlying variation in primary metabolism in potato (Solanum tuberosum), we have profiled primary metabolite content in a diploid potato mapping population, derived from crosses between S. tuberosum and wild relatives, using gas chromatography-time of flight-mass spectrometry. In total, 139 polar metabolites were detected, of which we identified metabolite quantitative trait loci for approximately 72% of the detected compounds. In order to obtain an insight into the relationships between metabolic traits and classical phenotypic traits, we also analyzed statistical associations between them. The combined analysis of genetic information through quantitative trait locus coincidence and the application of statistical learning methods provide information on putative indicators associated with the alterations in metabolic networks that affect complex phenotypic traits.
Collapse
|
40
|
Lidder P, Sonnino A. Biotechnologies for the management of genetic resources for food and agriculture. ADVANCES IN GENETICS 2012; 78:1-167. [PMID: 22980921 DOI: 10.1016/b978-0-12-394394-1.00001-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
In recent years, the land area under agriculture has declined as also has the rate of growth in agricultural productivity while the demand for food continues to escalate. The world population now stands at 7 billion and is expected to reach 9 billion in 2045. A broad range of agricultural genetic diversity needs to be available and utilized in order to feed this growing population. Climate change is an added threat to biodiversity that will significantly impact genetic resources for food and agriculture (GRFA) and food production. There is no simple, all-encompassing solution to the challenges of increasing productivity while conserving genetic diversity. Sustainable management of GRFA requires a multipronged approach, and as outlined in the paper, biotechnologies can provide powerful tools for the management of GRFA. These tools vary in complexity from those that are relatively simple to those that are more sophisticated. Further, advances in biotechnologies are occurring at a rapid pace and provide novel opportunities for more effective and efficient management of GRFA. Biotechnology applications must be integrated with ongoing conventional breeding and development programs in order to succeed. Additionally, the generation, adaptation, and adoption of biotechnologies require a consistent level of financial and human resources and appropriate policies need to be in place. These issues were also recognized by Member States at the FAO international technical conference on Agricultural Biotechnologies for Developing Countries (ABDC-10), which took place in March 2010 in Mexico. At the end of the conference, the Member States reached a number of key conclusions, agreeing, inter alia, that developing countries should significantly increase sustained investments in capacity building and the development and use of biotechnologies to maintain the natural resource base; that effective and enabling national biotechnology policies and science-based regulatory frameworks can facilitate the development and appropriate use of biotechnologies in developing countries; and that FAO and other relevant international organizations and donors should significantly increase their efforts to support the strengthening of national capacities in the development and appropriate use of pro-poor agricultural biotechnologies.
Collapse
Affiliation(s)
- Preetmoninder Lidder
- Office of Knowledge Exchange, Research and Extension, Research and Extension Branch, Food and Agriculture Organization of the UN (FAO), Viale delle Terme di Caracalla, Rome, Italy
| | - Andrea Sonnino
- Office of Knowledge Exchange, Research and Extension, Research and Extension Branch, Food and Agriculture Organization of the UN (FAO), Viale delle Terme di Caracalla, Rome, Italy
| |
Collapse
|
41
|
Ross HA, Morris WL, Ducreux LJM, Hancock RD, Verrall SR, Morris JA, Tucker GA, Stewart D, Hedley PE, McDougall GJ, Taylor MA. Pectin engineering to modify product quality in potato. PLANT BIOTECHNOLOGY JOURNAL 2011; 9:848-856. [PMID: 21281424 DOI: 10.1111/j.1467-7652.2011.00591.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Although processed potato tuber texture is an important trait that influences consumer preference, a detailed understanding of tuber textural properties at the molecular level is lacking. Previous work has identified tuber pectin methyl esterase (PME) activity as a potential factor impacting on textural properties, and the expression of a gene encoding an isoform of PME (PEST1) was associated with cooked tuber textural properties. In this study, a transgenic approach was undertaken to investigate further the impact of the PEST1 gene. Antisense and over-expressing potato lines were generated. In over-expressing lines, tuber PME activity was enhanced by up to 2.3-fold; whereas in antisense lines, PME activity was decreased by up to 62%. PME isoform analysis indicated that the PEST1 gene encoded one isoform of PME. Analysis of cell walls from tubers from the over-expressing lines indicated that the changes in PME activity resulted in a decrease in pectin methylation. Analysis of processed tuber texture demonstrated that the reduced level of pectin methylation in the over-expressing transgenic lines was associated with a firmer processed texture. Thus, there is a clear link between PME activity, pectin methylation and processed tuber textural properties.
Collapse
Affiliation(s)
- Heather A Ross
- Plant Products and Food Quality Programme, Scottish Crop Research Institute, Dundee, UK
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
42
|
Honkatukia M, Tuiskula-Haavisto M, Ahola V, Uimari P, Schmutz M, Preisinger R, Cavero D, Vennerström P, Arango J, O'Sullivan N, Fulton J, Vilkki J. Mapping of QTL affecting incidence of blood and meat inclusions in egg layers. BMC Genet 2011; 12:55. [PMID: 21668941 PMCID: PMC3145579 DOI: 10.1186/1471-2156-12-55] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2010] [Accepted: 06/13/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Occurrence of blood and meat inclusions is an internal egg quality defect. Mass candling reveals most of the spots, but because brown eggshell hampers selection in brown chicken lines it has not been possible to eliminate the defect by selection. Estimated frequency of blood and meat inclusions in brown layers is about 18% whereas it is 0.5% in white egg layers. Several factors are known to increase the incidence of this fault: genetic background, low level of vitamin A and/or D, stress or infections, for instance. To study the genetic background of the defect, a mapping population of 1599 F2 hens from a cross of White Rock and Rhode Island Red lines was set up. RESULTS Our histopathological analyses show that blood spots consist of mainly erythrocytes and that meat spots are accumulations of necrotic material. Linkage analysis of 27 chromosomes with 162 microsatellite markers revealed one significant quantitative trait locus (QTL) affecting blood spot and meat spot frequency. We sequenced a fragment of a candidate gene within the region, ZO-2, coding for a tight junction protein. Nine polymorphisms were detected and two of them were included in fine-mapping and association analysis. Fine-mapping defined the QTL result. To further verify the QTL, association analyses were carried out in two independent commercial breeding lines with the marker MCW241 and surrounding SNPs. Association was found mainly in a 0.8 Mb-wide chromosomal area on GGAZ. CONCLUSIONS There was good agreement between the location of the QTL region on chromosome Z and the association results in the commercial breeds analyzed. Variations found in tight junction protein ZO-2 and microRNA gga-mir-1556 may predispose egg layers to blood and meat spot defects. This paper describes the first results of detailed QTL analyses of the blood and meat spots trait(s) in chickens.
Collapse
Affiliation(s)
- Mervi Honkatukia
- Biotechnology and Food Research, MTT, Jokioinen, 31600, Finland.
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
43
|
Zhou X, McQuinn R, Fei Z, Wolters AMA, VAN Eck J, Brown C, Giovannoni JJ, Li LI. Regulatory control of high levels of carotenoid accumulation in potato tubers. PLANT, CELL & ENVIRONMENT 2011; 34:1020-1030. [PMID: 21388418 DOI: 10.1111/j.1365-3040.2011.02301.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Potato (Solanum tuberosum L.) tubers contain a wide range of carotenoid contents. To decipher the key factors controlling carotenoid levels in tubers, four potato lines (Atlantic, Désirée, 91E22 and POR03) were examined by a combination of biochemical, molecular and genomics approaches. These lines contained incremental levels of carotenoids, which were found to be associated with enhanced capacity of carotenoid biosynthesis as evident from norflurazon treatment. Microarray analysis of high and low carotenoid lines (POR03 versus Atlantic) revealed 381 genes that showed significantly differential expression. The carotenoid metabolic pathway genes β-carotene hydroxylase 2 (BCH2) and β-carotene hydroxylase 1 (BCH1), along with zeaxanthin epoxidase (ZEP), and carotenoid cleavage dioxygenase 1A (CCD1A) were among the most highly differentially expressed genes. The transcript levels of BCH2 and BCH1 were lowest in Atlantic and highest in POR03, whereas those of ZEP and CCD1A were high in low carotenoid lines and low in high carotenoid lines. The high expression of BCH2 in POR03 line was associated with enhanced response to sugars. Our results indicate that high levels of carotenoid accumulation in potato tubers were due to an increased metabolic flux into carotenoid biosynthetic pathway, as well as the differential expression of carotenoid metabolic genes.
Collapse
Affiliation(s)
- Xiangjun Zhou
- Robert W. Holley Center for Agriculture and Health, USDA-ARSDepartment of Plant Breeding and GeneticsBoyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY 14853, USALaboratory of Plant Breeding, Wageningen University, PO Box 386, 6700 AJ Wageningen, the NetherlandsUSDA-ARS, 24106 N. Bunn Road., Prosser, WA 99350, USA
| | - Ryan McQuinn
- Robert W. Holley Center for Agriculture and Health, USDA-ARSDepartment of Plant Breeding and GeneticsBoyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY 14853, USALaboratory of Plant Breeding, Wageningen University, PO Box 386, 6700 AJ Wageningen, the NetherlandsUSDA-ARS, 24106 N. Bunn Road., Prosser, WA 99350, USA
| | - Zhangjun Fei
- Robert W. Holley Center for Agriculture and Health, USDA-ARSDepartment of Plant Breeding and GeneticsBoyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY 14853, USALaboratory of Plant Breeding, Wageningen University, PO Box 386, 6700 AJ Wageningen, the NetherlandsUSDA-ARS, 24106 N. Bunn Road., Prosser, WA 99350, USA
| | - Anne-Marie A Wolters
- Robert W. Holley Center for Agriculture and Health, USDA-ARSDepartment of Plant Breeding and GeneticsBoyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY 14853, USALaboratory of Plant Breeding, Wageningen University, PO Box 386, 6700 AJ Wageningen, the NetherlandsUSDA-ARS, 24106 N. Bunn Road., Prosser, WA 99350, USA
| | - Joyce VAN Eck
- Robert W. Holley Center for Agriculture and Health, USDA-ARSDepartment of Plant Breeding and GeneticsBoyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY 14853, USALaboratory of Plant Breeding, Wageningen University, PO Box 386, 6700 AJ Wageningen, the NetherlandsUSDA-ARS, 24106 N. Bunn Road., Prosser, WA 99350, USA
| | - Charles Brown
- Robert W. Holley Center for Agriculture and Health, USDA-ARSDepartment of Plant Breeding and GeneticsBoyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY 14853, USALaboratory of Plant Breeding, Wageningen University, PO Box 386, 6700 AJ Wageningen, the NetherlandsUSDA-ARS, 24106 N. Bunn Road., Prosser, WA 99350, USA
| | - James J Giovannoni
- Robert W. Holley Center for Agriculture and Health, USDA-ARSDepartment of Plant Breeding and GeneticsBoyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY 14853, USALaboratory of Plant Breeding, Wageningen University, PO Box 386, 6700 AJ Wageningen, the NetherlandsUSDA-ARS, 24106 N. Bunn Road., Prosser, WA 99350, USA
| | - L I Li
- Robert W. Holley Center for Agriculture and Health, USDA-ARSDepartment of Plant Breeding and GeneticsBoyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY 14853, USALaboratory of Plant Breeding, Wageningen University, PO Box 386, 6700 AJ Wageningen, the NetherlandsUSDA-ARS, 24106 N. Bunn Road., Prosser, WA 99350, USA
| |
Collapse
|
44
|
Chen X, Hedley PE, Morris J, Liu H, Niks RE, Waugh R. Combining genetical genomics and bulked segregant analysis-based differential expression: an approach to gene localization. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2011; 122:1375-83. [PMID: 21267709 PMCID: PMC3075405 DOI: 10.1007/s00122-011-1538-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2010] [Accepted: 01/06/2011] [Indexed: 05/20/2023]
Abstract
Positional gene isolation in unsequenced species generally requires either a reference genome sequence or an inference of gene content based on conservation of synteny with a genomic model. In the large unsequenced genomes of the Triticeae cereals the latter, i.e. conservation of synteny with the rice and Brachypodium genomes, provides a powerful proxy for establishing local gene content and order. However, efficient exploitation of conservation of synteny requires 'homology bridges' between the model genome and the target region that contains a gene of interest. As effective homology bridges are generally the sequences of genetically mapped genes, increasing the density of these genes around a target locus is an important step in the process. We used bulked segregant analysis (BSA) of transcript abundance data to identify genes located in a specific region of the barley genome. The approach is valuable because only a relatively small proportion of barley genes are currently placed on a genetic map. We analyzed eQTL datasets from the reference Steptoe × Morex doubled haploid population and showed a strong association between differential gene expression and cis-regulation, with 83% of differentially expressed genes co-locating with their eQTL. We then performed BSA by assembling allele-specific pools based on the genotypes of individuals at the partial resistance QTL Rphq11. BSA identified a total of 411 genes as differentially expressed, including HvPHGPx, a gene previously identified as a promising candidate for Rphq11. The genetic location of 276 of these genes could be determined from both eQTL datasets and conservation of synteny, and 254 (92%) of these were located on the target chromosome. We conclude that the identification of differential expression by BSA constitutes a novel method to identify genes located in specific regions of interest. The datasets obtained from such studies provide a robust set of candidate genes for the analysis and serve as valuable resources for targeted marker development and comparative mapping with other grass species.
Collapse
Affiliation(s)
- Xinwei Chen
- Genetics Programme, Scottish Crop Research Institute, Invergowrie, Dundee, DD2 5DA Scotland, UK
| | - Peter E. Hedley
- Genetics Programme, Scottish Crop Research Institute, Invergowrie, Dundee, DD2 5DA Scotland, UK
| | - Jenny Morris
- Genetics Programme, Scottish Crop Research Institute, Invergowrie, Dundee, DD2 5DA Scotland, UK
| | - Hui Liu
- Genetics Programme, Scottish Crop Research Institute, Invergowrie, Dundee, DD2 5DA Scotland, UK
| | - Rients E. Niks
- Laboratory of Plant Breeding, Graduate School for Experimental Plant Sciences, Wageningen University, Wageningen, The Netherlands
| | - Robbie Waugh
- Genetics Programme, Scottish Crop Research Institute, Invergowrie, Dundee, DD2 5DA Scotland, UK
| |
Collapse
|
45
|
Acharjee A, Kloosterman B, de Vos RCH, Werij JS, Bachem CWB, Visser RGF, Maliepaard C. Data integration and network reconstruction with ~omics data using Random Forest regression in potato. Anal Chim Acta 2011; 705:56-63. [PMID: 21962348 DOI: 10.1016/j.aca.2011.03.050] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2010] [Revised: 03/23/2011] [Accepted: 03/25/2011] [Indexed: 10/18/2022]
Abstract
In the post-genomic era, high-throughput technologies have led to data collection in fields like transcriptomics, metabolomics and proteomics and, as a result, large amounts of data have become available. However, the integration of these ~omics data sets in relation to phenotypic traits is still problematic in order to advance crop breeding. We have obtained population-wide gene expression and metabolite (LC-MS) data from tubers of a diploid potato population and present a novel approach to study the various ~omics datasets to allow the construction of networks integrating gene expression, metabolites and phenotypic traits. We used Random Forest regression to select subsets of the metabolites and transcripts which show association with potato tuber flesh color and enzymatic discoloration. Network reconstruction has led to the integration of known and uncharacterized metabolites with genes associated with the carotenoid biosynthesis pathway. We show that this approach enables the construction of meaningful networks with regard to known and unknown components and metabolite pathways.
Collapse
Affiliation(s)
- Animesh Acharjee
- Graduate School Experimental Plant Sciences, Wageningen, The Netherlands.
| | | | | | | | | | | | | |
Collapse
|
46
|
Ross HA, Wright KM, McDougall GJ, Roberts AG, Chapman SN, Morris WL, Hancock RD, Stewart D, Tucker GA, James EK, Taylor MA. Potato tuber pectin structure is influenced by pectin methyl esterase activity and impacts on cooked potato texture. JOURNAL OF EXPERIMENTAL BOTANY 2011; 62:371-81. [PMID: 20855456 PMCID: PMC2993920 DOI: 10.1093/jxb/erq280] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Although cooked potato tuber texture is an important trait that influences consumer preference, a detailed understanding of tuber textural properties at the molecular level is lacking. Previous work has identified tuber pectin methyl esterase activity (PME) as a potential factor impacting on textural properties. In this study, tuber PME isoform and gene expression profiles have been determined in potato germplasm with differing textural properties as assessed using an amended wedge fracture method and a sloughing assay, revealing major differences between the potato types. Differences in pectin structure between potato types with different textural properties were revealed using monoclonal antibodies specific for different pectic epitopes. Chemical analysis of tuber pectin clearly demonstrated that, in tubers containing a higher level of total PME activity, there was a reduced degree of methylation of cell wall pectin and consistently higher peak force and work done values during the fracture of cooked tuber samples, demonstrating the link between PME activity, the degree of methylation of cell wall pectin, and cooked tuber textural properties.
Collapse
Affiliation(s)
- Heather A. Ross
- Plant Products and Food Quality Programme, Scottish Crop Research Institute, Dundee DD2 5DA, UK
| | - Kathryn M. Wright
- Cell Biology and Imaging, Plant Pathology Programme, Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Gordon J. McDougall
- Plant Products and Food Quality Programme, Scottish Crop Research Institute, Dundee DD2 5DA, UK
| | - Alison G. Roberts
- Cell Biology and Imaging, Plant Pathology Programme, Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Sean N. Chapman
- Cell Biology and Imaging, Plant Pathology Programme, Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Wayne L. Morris
- Plant Products and Food Quality Programme, Scottish Crop Research Institute, Dundee DD2 5DA, UK
| | - Robert D. Hancock
- Plant Products and Food Quality Programme, Scottish Crop Research Institute, Dundee DD2 5DA, UK
| | - Derek Stewart
- Plant Products and Food Quality Programme, Scottish Crop Research Institute, Dundee DD2 5DA, UK
| | - Gregory A. Tucker
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD, UK
| | - Euan K. James
- College of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Mark A. Taylor
- Plant Products and Food Quality Programme, Scottish Crop Research Institute, Dundee DD2 5DA, UK
- To whom correspondence should be addressed: E-mail:
| |
Collapse
|
47
|
Wolters AMA, Uitdewilligen JGAML, Kloosterman BA, Hutten RCB, Visser RGF, van Eck HJ. Identification of alleles of carotenoid pathway genes important for zeaxanthin accumulation in potato tubers. PLANT MOLECULAR BIOLOGY 2010; 73:659-71. [PMID: 20490894 PMCID: PMC2898108 DOI: 10.1007/s11103-010-9647-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2010] [Accepted: 04/30/2010] [Indexed: 05/04/2023]
Abstract
We have investigated the genetics and molecular biology of orange flesh colour in potato (Solanum tuberosum L.). To this end the natural diversity in three genes of the carotenoid pathway was assessed by SNP analyses. Association analysis was performed between SNP haplotypes and flesh colour phenotypes in diploid and tetraploid potato genotypes. We observed that among eleven beta-carotene hydroxylase 2 (Chy2) alleles only one dominant allele has a major effect, changing white into yellow flesh colour. In contrast, none of the lycopene epsilon cyclase (Lcye) alleles seemed to have a large effect on flesh colour. Analysis of zeaxanthin epoxidase (Zep) alleles showed that all (diploid) genotypes with orange tuber flesh were homozygous for one specific Zep allele. This Zep allele showed a reduced level of expression. The complete genomic sequence of the recessive Zep allele, including the promoter, was determined, and compared with the sequence of other Zep alleles. The most striking difference was the presence of a non-LTR retrotransposon sequence in intron 1 of the recessive Zep allele, which was absent in all other Zep alleles investigated. We hypothesise that the presence of this large sequence in intron 1 caused the lower expression level, resulting in reduced Zep activity and accumulation of zeaxanthin. Only genotypes combining presence of the dominant Chy2 allele with homozygosity for the recessive Zep allele produced orange-fleshed tubers that accumulated large amounts of zeaxanthin.
Collapse
Affiliation(s)
- Anne-Marie A Wolters
- Laboratory of Plant Breeding, Wageningen University, PO Box 386, 6700 AJ Wageningen, The Netherlands.
| | | | | | | | | | | |
Collapse
|