1
|
Mabry ME, Turner-Hissong SD, Gallagher EY, McAlvay AC, An H, Edger PP, Moore JD, Pink DAC, Teakle GR, Stevens CJ, Barker G, Labate J, Fuller DQ, Allaby RG, Beissinger T, Decker JE, Gore MA, Pires JC. The Evolutionary History of Wild, Domesticated, and Feral Brassica Oleracea (Brassicaceae). Mol Biol Evol 2021; 38:4419-4434. [PMID: 34157722 PMCID: PMC8476135 DOI: 10.1093/molbev/msab183] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Understanding the evolutionary history of crops, including identifying wild relatives, helps to provide insight for conservation and crop breeding efforts. Cultivated Brassica oleracea has intrigued researchers for centuries due to its wide diversity in forms, which include cabbage, broccoli, cauliflower, kale, kohlrabi, and Brussels sprouts. Yet, the evolutionary history of this species remains understudied. With such different vegetables produced from a single species, B. oleracea is a model organism for understanding the power of artificial selection. Persistent challenges in the study of B. oleracea include conflicting hypotheses regarding domestication and the identity of the closest living wild relative. Using newly generated RNA-seq data for a diversity panel of 224 accessions, which represents 14 different B. oleracea crop types and nine potential wild progenitor species, we integrate phylogenetic and population genetic techniques with ecological niche modeling, archaeological, and literary evidence to examine relationships among cultivars and wild relatives to clarify the origin of this horticulturally important species. Our analyses point to the Aegean endemic B. cretica as the closest living relative of cultivated B. oleracea, supporting an origin of cultivation in the Eastern Mediterranean region. Additionally, we identify several feral lineages, suggesting that cultivated plants of this species can revert to a wild-like state with relative ease. By expanding our understanding of the evolutionary history in B. oleracea, these results contribute to a growing body of knowledge on crop domestication that will facilitate continued breeding efforts including adaptation to changing environmental conditions.
Collapse
Affiliation(s)
- Makenzie E Mabry
- Division of Biological Sciences and Bond Life Sciences Center, University of Missouri, Columbia, MO, U.S.A
| | | | - Evan Y Gallagher
- Division of Biological Sciences and Bond Life Sciences Center, University of Missouri, Columbia, MO, U.S.A
| | - Alex C McAlvay
- Institute of Economic Botany, The New York Botanical Garden, Bronx, NY, U.S.A
| | - Hong An
- Division of Biological Sciences and Bond Life Sciences Center, University of Missouri, Columbia, MO, U.S.A
| | - Patrick P Edger
- Department of Horticulture, Michigan State University, MI, USA
| | | | - David A C Pink
- Agriculture and Environment Department, Harper Adams University, UK
| | | | - Chris J Stevens
- School of Archaeology and Museology, Peking University, Beijing, China.,Institute of Archaeology, University College London, London, UK
| | - Guy Barker
- School of Life Science, University of Warwick, UK
| | - Joanne Labate
- USDA, ARS Plant Genetic Resources Unit, Cornell AgriTech, Geneva, NY, USA
| | - Dorian Q Fuller
- Institute of Archaeology, University College London, London, UK.,School of Cultural Heritage, Northwest University, Xi'an, Shaanxi, China.,Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany
| | | | - Timothy Beissinger
- Division of Plant Breeding Methodology, Department of Crop Sciences, University of Goettingen, Goettingen, Germany
| | - Jared E Decker
- Division of Animal Sciences, University of Missouri, Columbia, USA
| | - Michael A Gore
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, U.S.A
| | - J Chris Pires
- Division of Biological Sciences and Bond Life Sciences Center, University of Missouri, Columbia, MO, U.S.A
| |
Collapse
|
2
|
Shu J, Liu Y, Li Z, Zhang L, Fang Z, Yang L, Zhuang M, Zhang Y, Lv H. Organelle Simple Sequence Repeat Markers Help to Distinguish Carpelloid Stamen and Normal Cytoplasmic Male Sterile Sources in Broccoli. PLoS One 2015; 10:e0138750. [PMID: 26407159 PMCID: PMC4583441 DOI: 10.1371/journal.pone.0138750] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 09/03/2015] [Indexed: 01/09/2023] Open
Abstract
We previously discovered carpelloid stamens when breeding cytoplasmic male sterile lines in broccoli (Brassica oleracea var. italica). In this study, hybrids and multiple backcrosses were produced from different cytoplasmic male sterile carpelloid stamen sources and maintainer lines. Carpelloid stamens caused dysplasia of the flower structure and led to hooked or coiled siliques with poor seed setting, which were inherited in a maternal fashion. Using four distinct carpelloid stamens and twelve distinct normal stamens from cytoplasmic male sterile sources and one maintainer, we used 21 mitochondrial simple sequence repeat (mtSSR) primers and 32 chloroplast SSR primers to identify a mitochondrial marker, mtSSR2, that can differentiate between the cytoplasm of carpelloid and normal stamens. Thereafter, mtSSR2 was used to identify another 34 broccoli accessions, with an accuracy rate of 100%. Analysis of the polymorphic sequences revealed that the mtSSR2 open reading frame of carpelloid stamen sterile sources had a deletion of 51 bases (encoding 18 amino acids) compared with normal stamen materials. The open reading frame is located in the coding region of orf125 and orf108 of the mitochondrial genomes in Brassica crops and had the highest similarity with Raphanus sativus and Brassica carinata. The current study has not only identified a useful molecular marker to detect the cytoplasm of carpelloid stamens during broccoli breeding, but it also provides evidence that the mitochondrial genome is maternally inherited and provides a basis for studying the effect of the cytoplasm on flower organ development in plants.
Collapse
Affiliation(s)
- Jinshuai Shu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, 12 Zhongguancun Nandajie Street, Beijing, 100081, China
| | - Yumei Liu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, 12 Zhongguancun Nandajie Street, Beijing, 100081, China
- * E-mail:
| | - Zhansheng Li
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, 12 Zhongguancun Nandajie Street, Beijing, 100081, China
| | - Lili Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, 12 Zhongguancun Nandajie Street, Beijing, 100081, China
| | - Zhiyuan Fang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, 12 Zhongguancun Nandajie Street, Beijing, 100081, China
| | - Limei Yang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, 12 Zhongguancun Nandajie Street, Beijing, 100081, China
| | - Mu Zhuang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, 12 Zhongguancun Nandajie Street, Beijing, 100081, China
| | - Yangyong Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, 12 Zhongguancun Nandajie Street, Beijing, 100081, China
| | - Honghao Lv
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, 12 Zhongguancun Nandajie Street, Beijing, 100081, China
| |
Collapse
|
3
|
Sarin B, Martín JP, Kaula BC, Mohanty A. Chloroplast DNA Variations in Wild Brassicas and Their Implication in Breeding and Population Genetics Studies. SCIENTIFICA 2015; 2015:952395. [PMID: 26347851 PMCID: PMC4546986 DOI: 10.1155/2015/952395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Accepted: 07/22/2015] [Indexed: 06/05/2023]
Abstract
Evaluation of chloroplast DNA (cpDNA) diversity in wild relatives of crop brassicas is important for characterization of cytoplasm and also for population genetics/phylogeographic analyses. The former is useful for breeding programs involving wide hybridization and synthesis of alloplasmic lines, while the latter is important for formulating conservation strategies. Therefore, PCR-RFLP (Polymerase Chain Reaction-Restriction Fragment Length Polymorphism) technique was applied to study cpDNA diversity in 14 wild brassicas (including 31 accessions) which revealed a total of 219 polymorphic fragments. The combination of polymorphisms obtained by using only two primer pair-restriction enzyme combinations was sufficient to distinguish all 14 wild brassicas. Moreover, 11 primer pairs-restriction enzyme combinations revealed intraspecific polymorphisms in eight wild brassicas (including endemic and endangered species, B. cretica and B. insularis, resp.). Thus, even within a small number of accessions that were screened, intraspecific polymorphisms were observed, which is important for population genetics analyses in wild brassicas and consequently for conservation studies.
Collapse
Affiliation(s)
- Bharti Sarin
- Department of Botany, Gargi College, University of Delhi, Sirifort Road, New Delhi 110049, India
| | - Juan Pedro Martín
- Departamento de Biología Vegetal, Escuela Técnica Superior de Ingenieros Agrónomos, Universidad Politécnica de Madrid, Ciudad Universitaria s/n, 28040 Madrid, Spain
| | - Babeeta Chrungu Kaula
- Department of Botany, Zakir Husain Delhi College, University of Delhi, Jawaharlal Nehru Marg, New Delhi 110002, India
| | - Aparajita Mohanty
- Department of Botany, Gargi College, University of Delhi, Sirifort Road, New Delhi 110049, India
| |
Collapse
|
4
|
Kalubi KN, Mehes-Smith M, Narendrula R, Michael P, Omri A. Molecular analysis of red maple (Acer rubrum) populations from a reclaimed mining region in Northern Ontario (Canada): soil metal accumulation and translocation in plants. ECOTOXICOLOGY (LONDON, ENGLAND) 2015; 24:636-647. [PMID: 25560741 DOI: 10.1007/s10646-014-1411-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 12/27/2014] [Indexed: 06/04/2023]
Abstract
Red maple (Acer rubrum) species is one of the most widespread deciduous (hardwood) trees of eastern North America. It is among the dominant tree species in the Northern Ontario after land reclamation. To date, the effects of heavy metal contamination from the mining activities on terrestrial ecosystems are not well understood. The main objectives of the present study are (1) to determine the level of phytoavailable metal in soil and accumulation in A. rubrum, and (2) to compare the levels of genetic variation among and within A. rubrum populations from areas with different metal contents in a Northern Ontario region. The total heavy metal levels were found to be high but the availability of these metals were much lower. We found that red maple does not accumulate heavy metals in their leaves as other hardwood species. The translocation factors were 0.05, 0.21, 0.38, 0.90, and 2.8 for Cu, Ni, Fe, Zn, and Mg, respectively. The levels of genetic variation in red maple populations from reclaimed lands in Northern Ontario were moderate to high since the percentage of polymorphic loci varied between 51 and 67%. The mean values for observed number of alleles (Na), effective number of alleles (Ne), Nei's gene diversity (h), and Shannon's information index (I) were 1.60, 1.24, 0.15 and 0.24, respectively. The population differentiation (GST) among the fragmented populations was high (0.28) despite a high level of gene flow (Nm = 1.28). Nevertheless, all the populations within the targeted region were genetically closely related. A specific ISSR marker that was identified in all the samples from the reference sites was absent in most samples from metal contaminated. This specific band was cloned and sequenced. Overall, the present study confirms that red maple populations in Northern Ontario are genetically sustainable despite the high level of total metal content in soil.
Collapse
Affiliation(s)
- K N Kalubi
- Department of Biology, Laurentian University, 935 Ramsey Lake Road, Sudbury, ON, P3E-2C6, Canada
| | | | | | | | | |
Collapse
|
5
|
Development of a chloroplast DNA marker for monitoring of transgene introgression in Brassica napus L. Biotechnol Lett 2013; 35:1533-9. [DOI: 10.1007/s10529-013-1236-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2013] [Accepted: 05/01/2013] [Indexed: 10/26/2022]
|
6
|
Yan GX, Wu XM, Li D, Zeng CL, Lv PJ, Gao GZ, Chen BY, Xu K, Lv XD. Assessing high-resolution melt curve analysis for accurate detection of DNA polymorphisms in the chloroplast gene accD of Crucifer species. BIOCHEM SYST ECOL 2012. [DOI: 10.1016/j.bse.2012.06.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
7
|
Zhang Y, Fang Z, Wang Q, Liu Y, Yang L, Zhuang M, Sun P. Chloroplast subspecies-specific SNP detection and its maternal inheritance in Brassica oleracea L. by using a dCAPS marker. ACTA ACUST UNITED AC 2012; 103:606-11. [PMID: 22577190 DOI: 10.1093/jhered/ess006] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Chloroplast simple sequence repeats amplicons in 5 subspecies of Brassica oleracea were sequenced, and one chloroplast SNP was detected in amplicon ACP43. Through the introduction of an RsaI recognition site by adding one mismatch in the forward primer, combined with the increased primer length and raised annealing temperature, the dCAPS (derived cleaved amplified polymorphic sequences) marker ACP43-93 RsaI was successfully developed. By using the dCAPS marker, the subspecies-specific SNP was assayed in 206 materials representing the wide distribution of B. oleracea. This is the first report of chloroplast DNA (cpDNA) variation in cultivated subspecies of B. oleracea, which showed that chloroplast diversity existed at the intersubspecies level. Unlike other subspecies, most of the broccoli and all of the cauliflower materials sharing the same haplotype showed closer relationships in cpDNA level. Furthermore, the dCAPS haplotype of the offspring from 7 male sterile backcross populations was the same as the female parents, indicating maternal inheritance.
Collapse
Affiliation(s)
- Yangyong Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | | | | | | | | | | | | |
Collapse
|
8
|
Allender CJ, Allainguillaume J, Lynn J, King GJ. Simple sequence repeats reveal uneven distribution of genetic diversity in chloroplast genomes of Brassica oleracea L. and (n = 9) wild relatives. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2007; 114:609-18. [PMID: 17143649 DOI: 10.1007/s00122-006-0461-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2006] [Accepted: 11/06/2006] [Indexed: 05/12/2023]
Abstract
Diversity in the chloroplast genome of 171 accessions representing the Brassica 'C' (n = 9) genome, including domesticated and wild B. oleracea and nine inter-fertile related wild species, was investigated using six chloroplast SSR (microsatellite) markers. The lack of diversity detected among 105 cultivated and wild accessions of B. oleracea contrasted starkly with that found within its wild relatives. The vast majority of B. oleracea accessions shared a single haplotype, whereas as many as six haplotypes were detected in two wild species, B. villosa Biv. and B. cretica Lam.. The SSRs proved to be highly polymorphic across haplotypes, with calculated genetic diversity values (H) of 0.23-0.87. In total, 23 different haplotypes were detected in C genome species, with an additional five haplotypes detected in B. rapa L. (A genome n = 10) and another in B. nigra L. (B genome, n = 8). The low chloroplast diversity of B. oleracea is not suggestive of multiple domestication events. The predominant B. oleracea haplotype was also common in B. incana Ten. and present in low frequencies in B. villosa, B. macrocarpa Guss, B. rupestris Raf. and B. cretica. The chloroplast SSRs reveal a wealth of diversity within wild Brassica species that will facilitate further evolutionary and phylogeographic studies of this important crop genus.
Collapse
Affiliation(s)
- C J Allender
- Warwick HRI, Wellesbourne, Warwick CV35 9EF, UK.
| | | | | | | |
Collapse
|
9
|
Flannery ML, Mitchell FJG, Coyne S, Kavanagh TA, Burke JI, Salamin N, Dowding P, Hodkinson TR. Plastid genome characterisation in Brassica and Brassicaceae using a new set of nine SSRs. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2006; 113:1221-31. [PMID: 16909279 DOI: 10.1007/s00122-006-0377-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2005] [Accepted: 07/15/2006] [Indexed: 05/09/2023]
Abstract
We report a new set of nine primer pairs specifically developed for amplification of Brassica plastid SSR markers. The wide utility of these markers is demonstrated for haplotype identification and detection of polymorphism in B. napus, B. nigra, B. oleracea, B. rapa and in related genera Arabidopsis, Camelina, Raphanus and Sinapis. Eleven gene regions (ndhB-rps7 spacer, rbcL-accD spacer, rpl16 intron, rps16 intron, atpB-rbcL spacer, trnE-trnT spacer, trnL intron, trnL-trnF spacer, trnM-atpE spacer, trnR-rpoC2 spacer, ycf3-psaA spacer) were sequenced from a range of Brassica and related genera for SSR detection and primer design. Other sequences were obtained from GenBank/EMBL. Eight out of nine selected SSR loci showed polymorphism when amplified using the new primers and a combined analysis detected variation within and between Brassica species, with the number of alleles detected per locus ranging from 5 (loci MF-6, MF-1) to 11 (locus MF-7). The combined SSR data were used in a neighbour-joining analysis (SMM, D (DM) distances) to group the samples based on the presence and absence of alleles. The analysis was generally able to separate plastid types into taxon-specific groups. Multi-allelic haplotypes were plotted onto the neighbour joining tree. A total number of 28 haplotypes were detected and these differentiated 22 of the 41 accessions screened from all other accessions. None of these haplotypes was shared by more than one species and some were not characteristic of their predicted type. We interpret our results with respect to taxon differentiation, hybridisation and introgression patterns relating to the 'Triangle of U'.
Collapse
Affiliation(s)
- M L Flannery
- Department of Botany, School of Natural Sciences, Trinity College, University of Dublin, Dublin, D2, Ireland
| | | | | | | | | | | | | | | |
Collapse
|