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Discovery of SNPs in important legumes through comparative genome analysis and conversion of SNPs into PCR-based markers. J Genet 2021. [DOI: 10.1007/s12041-021-01320-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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VanBuren R, Man Wai C, Wang X, Pardo J, Yocca AE, Wang H, Chaluvadi SR, Han G, Bryant D, Edger PP, Messing J, Sorrells ME, Mockler TC, Bennetzen JL, Michael TP. Exceptional subgenome stability and functional divergence in the allotetraploid Ethiopian cereal teff. Nat Commun 2020; 11:884. [PMID: 32060277 PMCID: PMC7021729 DOI: 10.1038/s41467-020-14724-z] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 01/30/2020] [Indexed: 12/22/2022] Open
Abstract
Teff (Eragrostis tef) is a cornerstone of food security in the Horn of Africa, where it is prized for stress resilience, grain nutrition, and market value. Here, we report a chromosome-scale assembly of allotetraploid teff (variety Dabbi) and patterns of subgenome dynamics. The teff genome contains two complete sets of homoeologous chromosomes, with most genes maintaining as syntenic gene pairs. TE analysis allows us to estimate that the teff polyploidy event occurred ~1.1 million years ago (mya) and that the two subgenomes diverged ~5.0 mya. Despite this divergence, we detect no large-scale structural rearrangements, homoeologous exchanges, or biased gene loss, in contrast to many other allopolyploids. The two teff subgenomes have partitioned their ancestral functions based on divergent expression across a diverse expression atlas. Together, these genomic resources will be useful for accelerating breeding of this underutilized grain crop and for fundamental insights into polyploid genome evolution.
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Affiliation(s)
- Robert VanBuren
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA.
- Plant Resilience Institute, Michigan State University, East Lansing, MI, 48824, USA.
| | - Ching Man Wai
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
- Plant Resilience Institute, Michigan State University, East Lansing, MI, 48824, USA
| | - Xuewen Wang
- Department of Genetics, University of Georgia, Athens, GA, 30602, USA
| | - Jeremy Pardo
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
- Plant Resilience Institute, Michigan State University, East Lansing, MI, 48824, USA
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Alan E Yocca
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Hao Wang
- Department of Genetics, University of Georgia, Athens, GA, 30602, USA
| | | | - Guomin Han
- Department of Genetics, University of Georgia, Athens, GA, 30602, USA
| | - Douglas Bryant
- Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA
| | - Patrick P Edger
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
| | - Joachim Messing
- Waksman Institute of Microbiology, Rutgers University, Springfield, USA
| | - Mark E Sorrells
- Department of Plant Breeding and Genetics, Cornell University, Ithaca, NY, USA
| | - Todd C Mockler
- Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA
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Chanyalew S, Ferede S, Damte T, Fikre T, Genet Y, Kebede W, Tolossa K, Tadele Z, Assefa K. Significance and prospects of an orphan crop tef. PLANTA 2019; 250:753-767. [PMID: 31222492 DOI: 10.1007/s00425-019-03209-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 06/05/2019] [Indexed: 06/09/2023]
Abstract
Tef is a resilient crop from the Horn of Africa with significant importance in food and nutrition security, and currently gaining global popularity as health and performance food. Tef [Eragrostis tef (Zucc.) Trotter] is the most important cereal of Ethiopia in terms of production, consumption and cash crop value. In Ethiopia, tef is annually grown on about 3 million ha with total grain production of over 5 million tons. As such, it accounts for about 30% of the total cultivated area and one-fifth of the gross grain production of all cereals cultivated in the country. In spite of its supreme economic and agricultural significance in Ethiopia, its productivity is relatively low with national average yield of about 1.7 t/ha. This has primarily been due to the very little scientific improvement done on the crop. Tef has still been an "orphan crop" since it is globally a very much under-researched crop owing to its localized importance. Scientific research on tef in Ethiopia began in the late 1950s. The main objective of this paper is to provide an overview of the significance and major production constraints of tef, and the major achievements made to date in various tef research aspects including breeding, agronomy, crop protection, and agricultural economics and extension. Based on these reviews, the paper eventually concludes with remarks on the way forward by emphasizing on the identification of the major gaps and the improvement efforts required for realizing the ever-needed breakthrough in the productivity and production of the crop. The major focal areas of future efforts include increasing productivity of both grain and biomass, systematic conservation and mining of the genetic resources, tackling the lodging malady, mechanization of the crop's husbandry, understanding the overall physiology of the crop especially with respect to stress tolerance, unraveling the nutritional qualities, and development of recipes and value-added products.
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Affiliation(s)
- Solomon Chanyalew
- Debre Zeit Agricultural Research Center, P.O. Box 32, Debre Zeit, Ethiopia
| | - Setotaw Ferede
- Debre Zeit Agricultural Research Center, P.O. Box 32, Debre Zeit, Ethiopia
| | - Tebkew Damte
- Debre Zeit Agricultural Research Center, P.O. Box 32, Debre Zeit, Ethiopia
| | - Tsion Fikre
- Debre Zeit Agricultural Research Center, P.O. Box 32, Debre Zeit, Ethiopia
| | - Yazachew Genet
- Debre Zeit Agricultural Research Center, P.O. Box 32, Debre Zeit, Ethiopia
| | - Worku Kebede
- Debre Zeit Agricultural Research Center, P.O. Box 32, Debre Zeit, Ethiopia
| | - Kidist Tolossa
- Debre Zeit Agricultural Research Center, P.O. Box 32, Debre Zeit, Ethiopia
| | - Zerihun Tadele
- Institute of Plant Sciences, University of Bern, Altenbergrain 21, 3013, Bern, Switzerland
| | - Kebebew Assefa
- Debre Zeit Agricultural Research Center, P.O. Box 32, Debre Zeit, Ethiopia.
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Bi R, Chandappa LH, Siddalingaiah L, Raju SKK, Balakrishna SH, Kumar J, Kuruba V, Hittalmani S. Leveraging barrel medic genome sequence for the development and use of genomic resources for genetic analysis and breeding in legumes. ELECTRON J BIOTECHN 2019. [DOI: 10.1016/j.ejbt.2019.02.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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Genotyping by Sequencing Reasserts the Close Relationship between Tef and Its Putative Wild Eragrostis Progenitors. DIVERSITY-BASEL 2018. [DOI: 10.3390/d10020017] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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Kamies R, Farrant JM, Tadele Z, Cannarozzi G, Rafudeen MS. A Proteomic Approach to Investigate the Drought Response in the Orphan Crop Eragrostis tef. Proteomes 2017; 5:E32. [PMID: 29140297 PMCID: PMC5748567 DOI: 10.3390/proteomes5040032] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Revised: 10/20/2017] [Accepted: 11/10/2017] [Indexed: 01/13/2023] Open
Abstract
The orphan crop, Eragrostis tef, was subjected to controlled drought conditions to observe the physiological parameters and proteins changing in response to dehydration stress. Physiological measurements involving electrolyte leakage, chlorophyll fluorescence and ultra-structural analysis showed tef plants tolerated water loss to 50% relative water content (RWC) before adverse effects in leaf tissues were observed. Proteomic analysis using isobaric tag for relative and absolute quantification (iTRAQ) mass spectrometry and appropriate database searching enabled the detection of 5727 proteins, of which 211 proteins, including a number of spliced variants, were found to be differentially regulated with the imposed stress conditions. Validation of the iTRAQ dataset was done with selected stress-related proteins, fructose-bisphosphate aldolase (FBA) and the protective antioxidant proteins, monodehydroascorbate reductase (MDHAR) and peroxidase (POX). Western blot analyses confirmed protein presence and showed increased protein abundance levels during water deficit while enzymatic activity for FBA, MDHAR and POX increased at selected RWC points. Gene ontology (GO)-term enrichment and analysis revealed terms involved in biotic and abiotic stress response, signaling, transport, cellular homeostasis and pentose metabolic processes, to be enriched in tef upregulated proteins, while terms linked to reactive oxygen species (ROS)-producing processes under water-deficit, such as photosynthesis and associated light harvesting reactions, manganese transport and homeostasis, the synthesis of sugars and cell wall catabolism and modification, to be enriched in tef downregulated proteins.
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Affiliation(s)
- Rizqah Kamies
- Department of Molecular and Cell Biology, University of Cape Town, Private Bag X3, Rondebosch 7701, South Africa.
| | - Jill M Farrant
- Department of Molecular and Cell Biology, University of Cape Town, Private Bag X3, Rondebosch 7701, South Africa.
| | - Zerihun Tadele
- Institute of Plant Sciences, University of Bern, Altenbergrain 21, 3013 Bern, Switzerland.
| | - Gina Cannarozzi
- Institute of Plant Sciences, University of Bern, Altenbergrain 21, 3013 Bern, Switzerland.
| | - Mohammed Suhail Rafudeen
- Department of Molecular and Cell Biology, University of Cape Town, Private Bag X3, Rondebosch 7701, South Africa.
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Cheng A, Mayes S, Dalle G, Demissew S, Massawe F. Diversifying crops for food and nutrition security - a case of teff. Biol Rev Camb Philos Soc 2015; 92:188-198. [PMID: 26456883 DOI: 10.1111/brv.12225] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Revised: 09/01/2015] [Accepted: 09/09/2015] [Indexed: 11/28/2022]
Abstract
There are more than 50000 known edible plants in the world, yet two-thirds of global plant-derived food is provided by only three major cereals - maize (Zea mays), wheat (Triticum aestivum) and rice (Oryza sativa). The dominance of this triad, now considered truly global food commodities, has led to a decline in the number of crop species contributing to global food supplies. Our dependence on only a few crop species limits our capability to deal with challenges posed by the adverse effects of climate change and the consequences of dietary imbalance. Emerging evidence suggests that climate change will cause shifts in crop production and yield loss due to more unpredictable and hostile weather patterns. One solution to this problem is through the wider use of underutilised (also called orphan or minor) crops to diversify agricultural systems and food sources. In addition to being highly nutritious, underutilised crops are resilient in natural and agricultural conditions, making them a suitable surrogate to the major crops. One such crop is teff [Eragrostis tef (Zucc.) Trotter], a warm-season annual cereal with the tiniest grain in the world. Native to Ethiopia and often the sustenance for local small farmers, teff thrives in both moisture-stressed and waterlogged soil conditions, making it a dependable staple within and beyond its current centre of origin. Today, teff is deemed a healthy wheat alternative in the West and is sought-after by health aficionados and those with coeliac disease or gluten sensitivity. The blooming market for healthy food is breathing new life into this underutilised crop, which has received relatively limited attention from mainstream research perhaps due to its 'orphan crop' status. This review presents the past, present and future of an ancient grain with a potential beyond its size.
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Affiliation(s)
- Acga Cheng
- Biotechnology Research Centre, School of Biosciences, The University of Nottingham Malaysia Campus, 43500, Semenyih, Selangor Darul Ehsan, Malaysia
| | - Sean Mayes
- Crops For the Future, The University of Nottingham Malaysia Campus, 43500, Semenyih, Selangor Darul Ehsan, Malaysia
| | - Gemedo Dalle
- Ethiopian Biodiversity Institute, P.O. Box 30726, Addis Ababa, Ethiopia
| | - Sebsebe Demissew
- The National Herbarium, Department of Plant Biology and Biodiversity Management, College of Natural Sciences, Addis Ababa University, P. O. Box 3434, Addis Ababa, Ethiopia
| | - Festo Massawe
- Biotechnology Research Centre, School of Biosciences, The University of Nottingham Malaysia Campus, 43500, Semenyih, Selangor Darul Ehsan, Malaysia.,Crops For the Future, The University of Nottingham Malaysia Campus, 43500, Semenyih, Selangor Darul Ehsan, Malaysia
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Assefa K, Cannarozzi G, Girma D, Kamies R, Chanyalew S, Plaza-Wüthrich S, Blösch R, Rindisbacher A, Rafudeen S, Tadele Z. Genetic diversity in tef [Eragrostis tef (Zucc.) Trotter]. FRONTIERS IN PLANT SCIENCE 2015; 6:177. [PMID: 25859251 PMCID: PMC4374454 DOI: 10.3389/fpls.2015.00177] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Accepted: 03/05/2015] [Indexed: 05/26/2023]
Abstract
Tef [Eragrostis tef (Zucc.) Trotter] is a cereal crop resilient to adverse climatic and soil conditions, and possessing desirable storage properties. Although tef provides high quality food and grows under marginal conditions unsuitable for other cereals, it is considered to be an orphan crop because it has benefited little from genetic improvement. Hence, unlike other cereals such as maize and wheat, the productivity of tef is extremely low. In spite of the low productivity, tef is widely cultivated by over six million small-scale farmers in Ethiopia where it is annually grown on more than three million hectares of land, accounting for over 30% of the total cereal acreage. Tef, a tetraploid with 40 chromosomes (2n = 4x = 40), belongs to the family Poaceae and, together with finger millet (Eleusine coracana Gaerth.), to the subfamily Chloridoideae. It was originated and domesticated in Ethiopia. There are about 350 Eragrostis species of which E. tef is the only species cultivated for human consumption. At the present time, the gene bank in Ethiopia holds over five thousand tef accessions collected from geographical regions diverse in terms of climate and elevation. These germplasm accessions appear to have huge variability with regard to key agronomic and nutritional traits. In order to properly utilize the variability in developing new tef cultivars, various techniques have been implemented to catalog the extent and unravel the patterns of genetic diversity. In this review, we show some recent initiatives investigating the diversity of tef using genomics, transcriptomics and proteomics and discuss the prospect of these efforts in providing molecular resources that can aid modern tef breeding.
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Affiliation(s)
- Kebebew Assefa
- National Tef Research Program, Debre Zeit Agricultural Research Center, Ethiopian Institute of Agricultural ResearchDebre Zeit, Ethiopia
| | - Gina Cannarozzi
- Crop Breeding and Genomics, Institute of Plant Sciences, Department of Biology, University of BernBern, Switzerland
| | - Dejene Girma
- Crop Breeding and Genomics, Institute of Plant Sciences, Department of Biology, University of BernBern, Switzerland
- National Agricultural Biotechnology Laboratory, Holetta Agricultural Research Center, Ethiopian Institute of Agricultural ResearchHoletta, Ethiopia
| | - Rizqah Kamies
- Plant Stress Laboratory, Department of Molecular and Cell Biology, University of Cape TownCape Town, South Africa
| | - Solomon Chanyalew
- National Tef Research Program, Debre Zeit Agricultural Research Center, Ethiopian Institute of Agricultural ResearchDebre Zeit, Ethiopia
| | - Sonia Plaza-Wüthrich
- Crop Breeding and Genomics, Institute of Plant Sciences, Department of Biology, University of BernBern, Switzerland
| | - Regula Blösch
- Crop Breeding and Genomics, Institute of Plant Sciences, Department of Biology, University of BernBern, Switzerland
| | - Abiel Rindisbacher
- Crop Breeding and Genomics, Institute of Plant Sciences, Department of Biology, University of BernBern, Switzerland
| | - Suhail Rafudeen
- Plant Stress Laboratory, Department of Molecular and Cell Biology, University of Cape TownCape Town, South Africa
| | - Zerihun Tadele
- Crop Breeding and Genomics, Institute of Plant Sciences, Department of Biology, University of BernBern, Switzerland
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Girma D, Assefa K, Chanyalew S, Cannarozzi G, Kuhlemeier C, Tadele Z. The origins and progress of genomics research on Tef (Eragrostis tef). PLANT BIOTECHNOLOGY JOURNAL 2014; 12:534-40. [PMID: 24891040 DOI: 10.1111/pbi.12199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Revised: 04/01/2014] [Accepted: 04/10/2014] [Indexed: 05/07/2023]
Abstract
Tef, Eragrostis tef (Zucc.) Trotter, is the most important cereal in Ethiopia. Tef is cultivated by more than five million small-scale farmers annually and constitutes the staple food for more than half of the population of 80 million. The crop is preferred by both farmers and consumers due to its beneficial traits associated with its agronomy and utilization. The genetic and phenotypic diversity of tef in Ethiopia is a national treasure of potentially global importance. In order for this diversity to be effectively conserved and utilized, a better understanding at the genomic level is necessary. In the recent years, tef has become the subject of genomic research in Ethiopia and abroad. Genomic-assisted tef improvement holds tremendous potential for improving productivity, thereby benefiting the smallholder farmers who have cultivated and relied on the crop for thousands of years. It is hoped that such research endeavours will provide solutions to some of the age-old problems of tef's husbandry. In this review, we provide a brief description of the genesis and progress of tef genomic research to date, suggest ways to utilize the genomic tools developed so far, discuss the potential of genomics to enable sustainable conservation and use of tef genetic diversity and suggest opportunities for the future research.
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Affiliation(s)
- Dejene Girma
- Institute of Plant Sciences, University of Bern, Bern, Switzerland; Ethiopian Institute of Agricultural Research, Debre Zeit Agricultural Research Centre, Debre Zeit, Ethiopia
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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.
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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:
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Haplotype Analysis and Linkage Disequilibrium at Five Loci in Eragrostis tef. G3-GENES GENOMES GENETICS 2012; 2:407-19. [PMID: 22413094 PMCID: PMC3291510 DOI: 10.1534/g3.111.001511] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2011] [Accepted: 01/20/2012] [Indexed: 01/08/2023]
Abstract
Eragrostis tef (Zucc.), a member of the Chloridoideae subfamily of grasses, is one of the most important food crops in Ethiopia. Lodging is the most important production problem in tef. The rht1 and sd1 dwarfing genes have been useful for improving lodging resistance in wheat and rice, respectively, in what has been known as the “Green Revolution.” All homologs of rht1 and sd1 were cloned and sequenced from 31 tef accessions collected from across Ethiopia. The allotetraploid tef genome was found to carry two rht1 homologs. From sequence variation between these two putative homologs, an approximate ancestral divergence date of 6.4 million years ago was calculated for the two genomes within tef. Three sd1 homologs were identified in tef, with unknown orthologous/paralogous relationships. The genetic diversity in the 31 studied accessions was organized into a relatively small number of haplotypes (2−4) for four of these genes, whereas one rht1 homeologue exhibited 10 haplotypes. A low level of nucleotide diversity was observed at all loci. Linkage disequilibrium analysis demonstrated strong linkage disequilibrium, extending the length of the five genes investigated (2−4 kb), with no significant decline. There was no significant correlation between haplotypes of any of these genes and their recorded site of origin.
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Zeid M, Belay G, Mulkey S, Poland J, Sorrells ME. QTL mapping for yield and lodging resistance in an enhanced SSR-based map for tef. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2011; 122:77-93. [PMID: 20706706 DOI: 10.1007/s00122-010-1424-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2010] [Accepted: 07/30/2010] [Indexed: 05/07/2023]
Abstract
Tef is a cereal crop of cultural and economic importance in Ethiopia. It is grown primarily for its grain though it is also an important source of fodder. Tef suffers from lodging that reduces both grain yield and quality. As a first step toward executing a marker-assisted breeding program for lodging resistance and grain yield improvement, a linkage map was constructed using 151 F(9) recombinant inbred lines obtained by single-seed-descent from a cross between Eragrostis tef and its wild relative Eragrostis pilosa. The map was primarily based on microsatellite (SSR) markers that were developed from SSR-enriched genomic libraries. The map consisted of 30 linkage groups and spanned a total length of 1,277.4 cM (78.7% of the genome) with an average distance of 5.7 cM between markers. This is the most saturated map for tef to date, and for the first time, all of the markers are PCR-based. Using agronomic data from 11 environments and marker data, it was possible to map quantitative trait loci (QTL) controlling lodging, grain yield and 15 other related traits. The positive effects of the QTL identified from the wild parent were mainly for earliness, reduced culm length and lodging resistance. In this population, it is now possible to combine lodging resistance and grain yield using a marker-assisted selection program targeting the QTL identified for both traits. The newly developed SSR markers will play a key role in germplasm organization, fingerprinting and monitoring the success of the hybridization process in intra-specific crosses lacking distinctive morphological markers.
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Affiliation(s)
- M Zeid
- Department of Plant Breeding and Genetics, Cornell University, 240 Emerson Hall, Ithaca, NY 14853, USA
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Sim SC, Yu JK, Jo YK, Sorrells ME, Jung G. Transferability of cereal EST-SSR markers to ryegrass. Genome 2009; 52:431-7. [PMID: 19448723 DOI: 10.1139/g09-019] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A large number of expressed sequence tags (ESTs) in public databases have provided an opportunity for the systematic development of simple sequence repeat (SSR) markers. EST-SSRs derived from conserved coding sequences show considerable cross-species transferability in related species. In the present study, we assessed the utility of cereal EST-SSRs in ryegrass (Lolium spp.). A total of 165 cereal EST-SSRs were tested; a high rate of transferability (57%) and polymorphism (67% of functional EST-SSRs) was demonstrated between cereals and ryegrass. A total of 46 segregating loci derived from 37 EST-SSRs were mapped on an existing ryegrass genetic map. The mapped loci were uniformly distributed across all seven linkage groups without significant clustering at the distal regions of linkage groups. Sequences of ryegrass amplicons generated by randomly selected 16 EST-SSRs were aligned with reference sequences of cereal EST-SSRs. The SSR motifs and repeat lengths of the cereal EST-SSR markers were different from the majority of ryegrass amplicons. Furthermore, a majority of EST-SSRs amplified different flanking sequences of SSRs in ryegrass than the original cereal sequences. Our results suggest that the high degree of cereal EST-SSR transferability to ryegrass can be a useful enhancement to the molecular database of PCR-based markers but sequence analysis is essential before transferring genetic information using comparative mapping.
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Affiliation(s)
- Sung-Chur Sim
- Department of Horticulture and Crop Science, Ohio State University, Ohio Agricultural Research and Development Center, Wooster, OH 44691, USA
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Venkatesan M, Broman KW, Sellers M, Rasgon JL. An initial linkage map of the West Nile Virus vector Culex tarsalis. INSECT MOLECULAR BIOLOGY 2009; 18:453-463. [PMID: 19453767 PMCID: PMC3668313 DOI: 10.1111/j.1365-2583.2009.00885.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
We have constructed the first genetic linkage map for the North American arboviral vector Culex tarsalis. 120 F(2) offspring from a cross between two colonies were genotyped using 25 microsatellites and six inter-simple sequence repeat (ISSR) markers. We resolved four linkage groups which likely correspond to two full-length chromosomes and two arms of the final chromosome. The longest linkage group contains the sex locus and corresponds to chromosome 3. Recombination rates around the sex locus were dramatically higher in females compared to males. The majority of microsatellite loci share sequence identity with regions of the Culex quinquefasciatus genome, whose assembly should aid in anchoring linkage groups to physical chromosomes. This map will aid in identification of loci involved with variable phenotypes in C. tarsalis including WNV susceptibility.
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Affiliation(s)
- M Venkatesan
- The W. Harry Feinstone Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland 21205, USA
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Abstract
Neurospora crassa has been a model organism for the study of circadian clocks for the past four decades. Among natural accessions of Neurospora crassa, there is significant variation in clock phenotypes. In an attempt to investigate natural allelic variants contributing to quantitative variation, we used a quantitative trait loci mapping approach to analyze three independent mapping populations whose progenitors were collected from geographically isolated locations. Two circadian clock phenotypes, free-running period and entrained phase, were evaluated in the 188 F(1) progeny of each mapping population. To identify the clock QTL, we applied two QTL mapping analyses: composite interval mapping (CIM) and Bayesian multiple QTL analysis (BMQ). When controlling false positive rates < or =0.05, BMQ appears to be the more sensitive of the two approaches. BMQ confirmed most of the QTL from CIM (18 QTL) and identified 23 additional QTL. While 13 QTL colocalize with previously identified clock genes, we identified 30 QTL that were not linked with any previously characterized clock genes. These are candidate regions where clock genes may be located and are expected to lead to new insights in clock regulation.
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16
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Lohithaswa HC, Feltus FA, Singh HP, Bacon CD, Bailey CD, Paterson AH. Leveraging the rice genome sequence for monocot comparative and translational genomics. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2007; 115:237-43. [PMID: 17522835 DOI: 10.1007/s00122-007-0559-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2006] [Accepted: 04/14/2007] [Indexed: 05/15/2023]
Abstract
Common genome anchor points across many taxa greatly facilitate translational and comparative genomics and will improve our understanding of the Tree of Life. To add to the repertoire of genomic tools applicable to the study of monocotyledonous plants in general, we aligned Allium and Musa ESTs to Oryza BAC sequences and identified candidate Allium-Oryza and Musa-Oryza conserved intron-scanning primers (CISPs). A random sampling of 96 CISP primer pairs, representing loci from 11 of the 12 chromosomes in rice, were tested on seven members of the order Poales and on representatives of the Arecales, Asparagales, and Zingiberales monocot orders. The single-copy amplification success rates of Allium (31.3%), Cynodon (31.4%), Hordeum (30.2%), Musa (37.5%), Oryza (61.5%), Pennisetum (33.3%), Sorghum (47.9%), Zea (33.3%), Triticum (30.2%), and representatives of the palm family (32.3%) suggest that subsets of these primers will provide DNA markers suitable for comparative and translational genomics in orphan crops, as well as for applications in conservation biology, ecology, invasion biology, population biology, systematic biology, and related fields.
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Affiliation(s)
- H C Lohithaswa
- Plant Genome Mapping Laboratory, University of Georgia, 111 Riverbend Road, Athens, GA 30602, USA
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17
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Yu JK, Graznak E, Breseghello F, Tefera H, Sorrells ME. QTL mapping of agronomic traits in tef [Eragrostis tef (Zucc) Trotter]. BMC PLANT BIOLOGY 2007; 7:30. [PMID: 17565675 PMCID: PMC1913516 DOI: 10.1186/1471-2229-7-30] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2006] [Accepted: 06/12/2007] [Indexed: 05/07/2023]
Abstract
BACKGROUND Tef [Eragrostis tef (Zucc.) Trotter] is the major cereal crop in Ethiopia. Tef is an allotetraploid with a base chromosome number of 10 (2n = 4x = 40) and a genome size of 730 Mbp. The goal of this study was to identify agronomically important quantitative trait loci (QTL) using recombinant inbred lines (RIL) derived from an inter-specific cross between E. tef and E. pilosa (30-5). RESULTS Twenty-two yield-related and morphological traits were assessed across eight different locations in Ethiopia during the growing seasons of 1999 and 2000. Using composite interval mapping and a linkage map incorporating 192 loci, 99 QTLs were identified on 15 of the 21 linkage groups for 19 traits. Twelve QTLs on nine linkage groups were identified for grain yield. Clusters of more than five QTLs for various traits were identified on seven linkage groups. The largest cluster (10 QTLs) was identified on linkage group 8; eight of these QTLs were for yield or yield components, suggesting linkage or pleotrophic effects of loci. There were 15 two-way interactions of loci to detect potential epistasis identified and 75% of the interactions were derived from yield and shoot biomass. Thirty-one percent of the QTLs were observed in multiple environments; two yield QTLs were consistent across all agro-ecology zones. For 29.3% of the QTLs, the alleles from E. pilosa (30-5) had a beneficial effect. CONCLUSION The extensive QTL data generated for tef in this study will provide a basis for initiating molecular breeding to improve agronomic traits in this staple food crop for the people of Ethiopia.
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Affiliation(s)
- Ju-Kyung Yu
- Department of Plant Breeding and Genetics, Cornell University, Ithaca NY 14853, USA
- Syngenta Seeds Inc. 317 330th Street, Stanton, MN 55018, USA
| | - Elizabeth Graznak
- Department of Plant Breeding and Genetics, Cornell University, Ithaca NY 14853, USA
| | - Flavio Breseghello
- Department of Plant Breeding and Genetics, Cornell University, Ithaca NY 14853, USA
- Embrapa Arroze Feijão, Caixa Postal 179, Santo Antônio de Goiás, GO 75375-000, Brazil
| | - Hailu Tefera
- Debre Zeit Agricultural Research Center, P.O. Box 32, Debre Zeit, Ethiopia
| | - Mark E Sorrells
- Department of Plant Breeding and Genetics, Cornell University, Ithaca NY 14853, USA
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