1
|
Li Z, Liu Y, Yuan S, Han F, Fang Z, Yang L, Zhuang M, Zhang Y, Lv H, Wang Y, Ji J. Fine mapping of the major QTLs for biochemical variation of sulforaphane in broccoli florets using a DH population. Sci Rep 2021; 11:9004. [PMID: 33903705 PMCID: PMC8076207 DOI: 10.1038/s41598-021-88652-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Accepted: 04/15/2021] [Indexed: 11/09/2022] Open
Abstract
Glucoraphanin is a major secondary metabolite found in Brassicaceae vegetables, especially broccoli, and its degradation product sulforaphane plays an essential role in anticancer. The fine mapping of sulforaphane metabolism quantitative trait loci (QTLs) in broccoli florets is necessary for future marker-assisted selection strategies. In this study, we utilized a doubled haploid population consisting of 176 lines derived from two inbred lines (86,101 and 90,196) with significant differences in sulforaphane content, coupled with extensive genotypic and phenotypic data from two independent environments. A linkage map consisting of 438 simple sequence repeats markers was constructed, covering a length of 1168.26 cM. A total of 18 QTLs for sulforaphane metabolism in broccoli florets were detected, 10 were detected in 2017, and the other 8 were detected in 2018. The LOD values of all QTLs ranged from 3.06 to 14.47, explaining 1.74-7.03% of the biochemical variation between two years. Finally, 6 QTLs (qSF-C3-1, qSF-C3-2, qSF-C3-3, qSF-C3-5, qSF-C3-6 and qSF-C7) were stably detected in more than one environment, each accounting for 4.54-7.03% of the phenotypic variation explained (PVE) and a total of 30.88-34.86% of PVE. Our study provides new insights into sulforaphane metabolism in broccoli florets and marker-assisted selection breeding in Brassica oleracea crops.
Collapse
Affiliation(s)
- Zhansheng Li
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China.
| | - Yumei Liu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Suxia Yuan
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Fengqing Han
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhiyuan Fang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Limei Yang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Mu Zhuang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yangyong Zhang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Honghao Lv
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yong Wang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jialei Ji
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| |
Collapse
|
2
|
Raman H, Raman R, McVittie B, Orchard B, Qiu Y, Delourme R. A Major Locus for Manganese Tolerance Maps on Chromosome A09 in a Doubled Haploid Population of Brassica napus L. FRONTIERS IN PLANT SCIENCE 2017; 8:1952. [PMID: 29312361 PMCID: PMC5733045 DOI: 10.3389/fpls.2017.01952] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Accepted: 10/30/2017] [Indexed: 05/09/2023]
Abstract
Soil acidity poses a major threat to productivity of several crops; mainly due to the prevalence of toxic levels of Al3+ and Mn2+. Crop productivity could be harnessed on acid soils via the development of plant varieties tolerant to phytotoxic levels of these cations. In this study, we investigated the extent of natural variation for Mn2+ tolerance among ten parental lines of the Australian and International canola mapping populations. Response to Mn2+ toxicity was measured on the bases of cotyledon chlorosis, shoot biomass, and leaf area in nutrient solution under control (9 μM of MnCl2⋅4H2O) and Mn treatment (125 μM of MnCl2⋅4H2O). Among parental lines, we selected Darmor-bzh and Yudal that showed significant and contrasting variation in Mn2+ tolerance to understand genetic control and identify the quantitative trait loci (QTL) underlying Mn2+ tolerance. We evaluated parental lines and their doubled haploid (DH) progenies (196 lines) derived from an F1 cross, Darmor-bzh/Yudal for Mn2+ tolerance. Mn2+-tolerant genotypes had significantly higher shoot biomass and leaf area compared to Mn2+-sensitive genotypes. A genetic linkage map based on 7,805 DArTseq markers corresponding to 2,094 unique loci was constructed and further utilized for QTL identification. A major locus, BnMn2+.A09 was further mapped with a SNP marker, Bn-A09-p29012402 (LOD score of 34.6) accounting for most of the variation in Mn2+ tolerance on chromosome A09. This is the first report on the genomic localization of a Mn2+ tolerance locus in B. napus. Additionally, an ortholog of A. thaliana encoding for cation efflux facilitator transporter was located within 3,991 bp from significant SNP marker associated with BnMn2+.A09. A suite of genome sequence based markers (DArTseq and Illumina Infinium SNPs) flanking the BnMn2+.A09 locus would provide an invaluable tool for various molecular breeding applications to improve canola production and profitability on Mn2+ toxic soils.
Collapse
Affiliation(s)
- Harsh Raman
- New South Wales Department of Primary Industries, Wagga Wagga Agricultural Institute, Wagga Wagga, NSW, Australia
- *Correspondence: Harsh Raman,
| | - Rosy Raman
- New South Wales Department of Primary Industries, Wagga Wagga Agricultural Institute, Wagga Wagga, NSW, Australia
| | - Brett McVittie
- New South Wales Department of Primary Industries, Wagga Wagga Agricultural Institute, Wagga Wagga, NSW, Australia
| | - Beverley Orchard
- New South Wales Department of Primary Industries, Wagga Wagga Agricultural Institute, Wagga Wagga, NSW, Australia
| | - Yu Qiu
- New South Wales Department of Primary Industries, Wagga Wagga Agricultural Institute, Wagga Wagga, NSW, Australia
| | - Regine Delourme
- INRA, Agrocampus Ouest, Université de Rennes 1, UMR1349 Institut de Génétique, Environnement et de Protection des Plantes, Le Rheu, France
| |
Collapse
|
3
|
Yang Y, Zhao Q, Li X, Ai W, Liu D, Qi W, Zhang M, Yang C, Liao H. Characterization of Genetic Basis on Synergistic Interactions between Root Architecture and Biological Nitrogen Fixation in Soybean. FRONTIERS IN PLANT SCIENCE 2017; 8:1466. [PMID: 28878798 PMCID: PMC5572596 DOI: 10.3389/fpls.2017.01466] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 08/07/2017] [Indexed: 05/23/2023]
Abstract
Soybean [Glycine max (L.) Merr] is an important legume crop and its yield largely depends on root architecture (RA) and biological nitrogen fixation (BNF). However, the relationship between RA and BNF, and its genetics behind remain unclear. Here, two soybean genotypes contrasting in RA and their 175 F9:11 recombinant inbred lines (RILs) were evaluated in field. The shallow-root parent, JD12, had better nodulation and higher yield than the deep-root parent, NF58. Strong correlations between shoot dry weight (SDW) and RA or BNF traits existed in the RILs, and the shallow-root group had more and heavier nodules, as well as higher SDW. After inoculating with rhizobia, roots became shallower and bigger, showing strong synergistic interactions between RA and BNF. In total, 70 QTLs were identified for the 21 tested traits. Among them, qBNF-RA-C2, qBNF-RA-O, and qBNF-RA-B1, were newly identified QTLs for BNF and/or RA traits in soybean, which co-located with the QTLs for SDW detected presently, and with the QTLs for yield identified previously. The results together suggest that there are synergistic interactions between RA and BNF, and the QTLs identified here could be used for breeding new soybean varieties with higher yields through optimization of RA traits and BNF capacity.
Collapse
Affiliation(s)
- Yongqing Yang
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Crop Science, Fujian Agriculture and Forestry UniversityFuzhou, China
- Root Biology Center, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Qingsong Zhao
- The Key Laboratory of Crop Genetics and Breeding of Hebei, Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry SciencesShijiazhuang, China
| | - Xinxin Li
- Root Biology Center, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Wenqin Ai
- Root Biology Center, Fujian Agriculture and Forestry UniversityFuzhou, China
- Root Biology Center, South China Agricultural UniversityGuangzhou, China
| | - Dong Liu
- Root Biology Center, Fujian Agriculture and Forestry UniversityFuzhou, China
- Root Biology Center, South China Agricultural UniversityGuangzhou, China
| | - Wandong Qi
- Root Biology Center, Fujian Agriculture and Forestry UniversityFuzhou, China
- Root Biology Center, South China Agricultural UniversityGuangzhou, China
| | - Mengchen Zhang
- The Key Laboratory of Crop Genetics and Breeding of Hebei, Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry SciencesShijiazhuang, China
| | - Chunyan Yang
- The Key Laboratory of Crop Genetics and Breeding of Hebei, Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry SciencesShijiazhuang, China
- *Correspondence: Chunyan Yang, Hong Liao, ;
| | - Hong Liao
- Root Biology Center, Fujian Agriculture and Forestry UniversityFuzhou, China
- *Correspondence: Chunyan Yang, Hong Liao, ;
| |
Collapse
|
4
|
Raman H, Raman R, Coombes N, Song J, Diffey S, Kilian A, Lindbeck K, Barbulescu DM, Batley J, Edwards D, Salisbury PA, Marcroft S. Genome-wide Association Study Identifies New Loci for Resistance to Leptosphaeria maculans in Canola. FRONTIERS IN PLANT SCIENCE 2016; 7:1513. [PMID: 27822217 PMCID: PMC5075532 DOI: 10.3389/fpls.2016.01513] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2016] [Accepted: 09/23/2016] [Indexed: 05/18/2023]
Abstract
Key message "We identified both quantitative and quantitative resistance loci to Leptosphaeria maculans, a fungal pathogen, causing blackleg disease in canola. Several genome-wide significant associations were detected at known and new loci for blackleg resistance. We further validated statistically significant associations in four genetic mapping populations, demonstrating that GWAS marker loci are indeed associated with resistance to L. maculans. One of the novel loci identified for the first time, Rlm12, conveys adult plant resistance in canola." Blackleg, caused by Leptosphaeria maculans, is a significant disease which affects the sustainable production of canola (Brassica napus). This study reports a genome-wide association study based on 18,804 polymorphic SNPs to identify loci associated with qualitative and quantitative resistance to L. maculans. Genomic regions delimited with 694 significant SNP markers, that are associated with resistance evaluated using 12 single spore isolates and pathotypes from four canola stubble were identified. Several significant associations were detected at known disease resistance loci including in the vicinity of recently cloned Rlm2/LepR3 genes, and at new loci on chromosomes A01/C01, A02/C02, A03/C03, A05/C05, A06, A08, and A09. In addition, we validated statistically significant associations on A01, A07, and A10 in four genetic mapping populations, demonstrating that GWAS marker loci are indeed associated with resistance to L. maculans. One of the novel loci identified for the first time, Rlm12, conveys adult plant resistance and mapped within 13.2 kb from Arabidopsis R gene of TIR-NBS class. We showed that resistance loci are located in the vicinity of R genes of Arabidopsis thaliana and Brassica napus on the sequenced genome of B. napus cv. Darmor-bzh. Significantly associated SNP markers provide a valuable tool to enrich germplasm for favorable alleles in order to improve the level of resistance to L. maculans in canola.
Collapse
Affiliation(s)
- Harsh Raman
- Graham Centre for Agricultural Innovation (an alliance between NSW Department of Primary Industries and Charles Sturt University), Wagga Wagga Agricultural Institute, Wagga WaggaNSW, Australia
| | - Rosy Raman
- Graham Centre for Agricultural Innovation (an alliance between NSW Department of Primary Industries and Charles Sturt University), Wagga Wagga Agricultural Institute, Wagga WaggaNSW, Australia
| | - Neil Coombes
- Graham Centre for Agricultural Innovation (an alliance between NSW Department of Primary Industries and Charles Sturt University), Wagga Wagga Agricultural Institute, Wagga WaggaNSW, Australia
| | - Jie Song
- Diversity Array Technology P/L, University of Canberra, CanberraACT, Australia
| | - Simon Diffey
- Centre for Bioinformatics and Biometrics, University of Wollongong, WollongongNSW, Australia
| | - Andrzej Kilian
- Diversity Array Technology P/L, University of Canberra, CanberraACT, Australia
| | - Kurt Lindbeck
- Graham Centre for Agricultural Innovation (an alliance between NSW Department of Primary Industries and Charles Sturt University), Wagga Wagga Agricultural Institute, Wagga WaggaNSW, Australia
| | - Denise M. Barbulescu
- Department of Economic Development, Jobs, Transport and Resources, HorshamVIC, Australia
| | - Jacqueline Batley
- School of Plant Biology, University of Western Australia, CrawleyWA, Australia
| | - David Edwards
- School of Plant Biology, University of Western Australia, CrawleyWA, Australia
- Institute of Agriculture, University of Western Australia, CrawleyWA, Australia
| | - Phil A. Salisbury
- Department of Economic Development, Jobs, Transport and Resources, HorshamVIC, Australia
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, ParkvilleVIC, Australia
| | | |
Collapse
|
5
|
Colasuonno P, Maria MA, Blanco A, Gadaleta A. Description of durum wheat linkage map and comparative sequence analysis of wheat mapped DArT markers with rice and Brachypodium genomes. BMC Genet 2013; 14:114. [PMID: 24304553 PMCID: PMC3866978 DOI: 10.1186/1471-2156-14-114] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Accepted: 11/25/2013] [Indexed: 01/29/2023] Open
Abstract
Background The importance of wheat to the world economy, together with progresses in high-throughput next-generation DNA sequencing, have accelerated initiatives of genetic research for wheat improvement. The availability of high density linkage maps is crucial to identify genotype-phenotype associations, but also for anchoring BAC contigs to genetic maps, a strategy followed for sequencing the wheat genome. Results Here we report a genetic linkage map in a durum wheat segregating population and the study of mapped DArT markers. The linkage map consists of 126 gSSR, 31 EST-SSR and 351 DArT markers distributed in 24 linkage groups for a total length of 1,272 cM. Through bioinformatic approaches we have analysed 327 DArT clones to reveal their redundancy, syntenic and functional aspects. The DNA sequences of 174 DArT markers were assembled into a non-redundant set of 60 marker clusters. This explained the generation of clusters in very small chromosome regions across genomes. Of these DArT markers, 61 showed highly significant (Expectation < E-10) BLAST similarity to gene sequences in public databases of model species such as Brachypodium and rice. Based on sequence alignments, the analysis revealed a mosaic gene conservation, with 54 and 72 genes present in rice and Brachypodium species, respectively. Conclusions In the present manuscript we provide a detailed DArT markers characterization and the basis for future efforts in durum wheat map comparing.
Collapse
Affiliation(s)
| | | | | | - Agata Gadaleta
- Department of Soil, Plant and Food Sciences, University of Bari "Aldo Moro", Via Amendola 165/A, Bari 70126, Italy.
| |
Collapse
|
6
|
Hearnden PR, Eckermann PJ, McMichael GL, Hayden MJ, Eglinton JK, Chalmers KJ. A genetic map of 1,000 SSR and DArT markers in a wide barley cross. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2007; 115:383-91. [PMID: 17639300 DOI: 10.1007/s00122-007-0572-7] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2006] [Accepted: 04/25/2007] [Indexed: 05/10/2023]
Abstract
A high-density genetic map was developed from an F1-derived doubled haploid population generated from a cross between cultivated barley (Hordeum vulgare) and the subspecies H. vulgare ssp. spontaneum. The map comprises 1,000 loci, amplified using 536 SSR (558 loci) and 442 DArT markers. Of the SSRs, 149 markers (153 loci) were derived from barley ESTs, and 7 from wheat ESTs. A high level of polymorphism ( approximately 70%) was observed, which facilitated the mapping of 197 SSRs for which genetic assignments had not been previously reported. Comparison with a published composite map showed a high level of co-linearity and telomeric coverage on all seven chromosomes. This map provides access to previously unmapped SSRs, improved genome coverage due to the integration of DArT and EST-SSRs and overcomes locus order issues of composite maps constructed from the alignment of several genetic maps.
Collapse
Affiliation(s)
- P R Hearnden
- Molecular Plant Breeding Cooperative Research Centre (MPBCRC), PMB 1 Glen Osmond, Adelaide, SA 5064, Australia.
| | | | | | | | | | | |
Collapse
|