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Zhang F, Liu N, Chen T, Xu H, Li R, Wang L, Zhou S, Cai Q, Hou X, Wang L, Qian X, Zhu Z, Zhou K. Genome-wide identification of GH28 family and insight into its contributions to pod shattering resistance in Brassica napus L. BMC Genomics 2024; 25:492. [PMID: 38760719 PMCID: PMC11102225 DOI: 10.1186/s12864-024-10406-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Accepted: 05/13/2024] [Indexed: 05/19/2024] Open
Abstract
Rapeseed (Brassica napus L.), accounts for nearly 16% of vegetable oil, is the world's second produced oilseed. However, pod shattering has caused significant yield loses in rapeseed production, particularly during mechanical harvesting. The GH28 genes can promote pod shattering by changing the structure of the pod cell wall in Arabidopsis. However, the role of the GH28 gene family in rapeseed was largely unknown. Therefore, a genome-wide comprehensive analysis was conducted to classify the role of GH28 gene family on rapeseed pod shattering. A total of 37 BnaGH28 genes in the rapeseed genome were identified. These BnaGH28s can be divided into five groups (Group A-E), based on phylogenetic and synteny analysis. Protein property, gene structure, conserved motif, cis-acting element, and gene expression profile of BnaGH28 genes in the same group were similar. Specially, the expression level of genes in group A-D was gradually decreased, but increased in group E with the development of silique. Among eleven higher expressed genes in group E, two BnaGH28 genes (BnaA07T0199500ZS and BnaC06T0206500ZS) were significantly regulated by IAA or GA treatment. And the significant effects of BnaA07T0199500ZS variation on pod shattering resistance were also demonstrated in present study. These results could open a new window for insight into the role of BnaGH28 genes on pod shattering resistance in rapeseed.
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Affiliation(s)
- Fugui Zhang
- College of Agronomy, Anhui Agricultural University, 130, Changjiang West Road, Hefei, Anhui, 230036, China
| | - Nian Liu
- College of Agronomy, Anhui Agricultural University, 130, Changjiang West Road, Hefei, Anhui, 230036, China
| | - Tianhua Chen
- College of Agronomy, Anhui Agricultural University, 130, Changjiang West Road, Hefei, Anhui, 230036, China
| | - Hong Xu
- College of Agronomy, Anhui Agricultural University, 130, Changjiang West Road, Hefei, Anhui, 230036, China
| | - Rui Li
- College of Agronomy, Anhui Agricultural University, 130, Changjiang West Road, Hefei, Anhui, 230036, China
| | - Liyan Wang
- College of Agronomy, Anhui Agricultural University, 130, Changjiang West Road, Hefei, Anhui, 230036, China
| | - Shuo Zhou
- College of Agronomy, Anhui Agricultural University, 130, Changjiang West Road, Hefei, Anhui, 230036, China
| | - Qing'ao Cai
- College of Agronomy, Anhui Agricultural University, 130, Changjiang West Road, Hefei, Anhui, 230036, China
| | - Xinzhe Hou
- College of Agronomy, Anhui Agricultural University, 130, Changjiang West Road, Hefei, Anhui, 230036, China
| | - Ling Wang
- College of Agronomy, Anhui Agricultural University, 130, Changjiang West Road, Hefei, Anhui, 230036, China
| | - Xingzhi Qian
- College of Agronomy, Anhui Agricultural University, 130, Changjiang West Road, Hefei, Anhui, 230036, China
| | - Zonghe Zhu
- College of Agronomy, Anhui Agricultural University, 130, Changjiang West Road, Hefei, Anhui, 230036, China
| | - Kejin Zhou
- College of Agronomy, Anhui Agricultural University, 130, Changjiang West Road, Hefei, Anhui, 230036, China.
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Istaitieh M, Yoosefzadeh Najafabadi M, Edwards AM, Todd J, Van Acker R, Rajcan I. Genetic study for seed germination and shattering in Euphorbia lagascae in response to different seed treatments. Heliyon 2024; 10:e27975. [PMID: 38560240 PMCID: PMC10979140 DOI: 10.1016/j.heliyon.2024.e27975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 02/24/2024] [Accepted: 03/08/2024] [Indexed: 04/04/2024] Open
Abstract
Euphorbia lagascae Spreng is a promising emerging oilseed crop, with its seed oil accounting for approximately 50% of the seed weight. Euphorbia oil contains a significant amount of vernolic acid, comprising two-thirds of its composition, which boasts various industrial applications, including acting as a stabilizer-plasticizer and natural dye. However, this species was known to have a high degree of seed-shattering and a low germination rate, which act as two important barriers to large-scale production and exploitation. Therefore, the objective of this study is to determine the genetic control of seed germination and seed-shattering traits in order to develop a reliable pipeline that would be applicable for industries and breeders to select superior E. lagascae lines and design a robust breeding scheme in a short time at reduced labor costs. For this objective, five different wild-type genotypes of E. lagascae that demonstrated high germination potential were crossed with an ethyl methanesulfonate (EMS) mutant genotype that produces non-shattering capsules. The F2 populations from two successful crosses (A and B) were separated into three different treated groups for seed germination evaluation and to study the segregation of 200 individuals per F2 population. The three treatments were: light, gibberellic acid (GA3), and control treatment. Consequently, plants treated with approximately 250 μmol/m2/s of light showed significant improvement in germination up to 75% in cross A and 82.4 % in cross B compared with the control plants and the group treated with 0.05% GA3. According to the chi-square test results, the inheritance pattern of seed germination in response to light treatment follows a 3:1 segregation ratio between germinated and non-germinated seeds, indicating a dominant gene action in the F2 generation. The same conclusion was followed for the shattering trait in the group treated with light, which was also simply inherited as a 3:1 ratio for shattering vs. non-shattering capsules. Our results emphasize the importance and significance of light treatment in producing uniform populations through acceptable germination and shattering resistance of the mutant genotypes of E. lagascae. This is the first report of light treatment that significantly improved seed germination of E. lagascae, which may enhance efforts in the development of this new industrial crop as a feedstock for vernolic acid production.
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Affiliation(s)
- Maram Istaitieh
- Department of Plant Agriculture, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | | | - A. Michelle Edwards
- Office of Research, Ontario Agri-Food Innovation Alliance, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Jim Todd
- Ontario Ministry of Agriculture, Food and Rural Affairs, 1283 Blueline Rd, Simcoe, ON, N3Y 4K3, Canada
| | - Rene Van Acker
- Department of Plant Agriculture, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Istvan Rajcan
- Department of Plant Agriculture, University of Guelph, Guelph, ON, N1G 2W1, Canada
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Ohm H, Åstrand J, Ceplitis A, Bengtsson D, Hammenhag C, Chawade A, Grimberg Å. Novel SNP markers for flowering and seed quality traits in faba bean ( Vicia faba L.): characterization and GWAS of a diversity panel. FRONTIERS IN PLANT SCIENCE 2024; 15:1348014. [PMID: 38510437 PMCID: PMC10950902 DOI: 10.3389/fpls.2024.1348014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 02/21/2024] [Indexed: 03/22/2024]
Abstract
Faba bean (Vicia faba L.) is a legume crop grown in diverse climates worldwide. It has a high potential for increased cultivation to meet the need for more plant-based proteins in human diets, a prerequisite for a more sustainable food production system. Characterization of diversity panels of crops can identify variation in and genetic markers for target traits of interest for plant breeding. In this work, we collected a diversity panel of 220 accessions of faba bean from around the world consisting of gene bank material and commercially available cultivars. The aims of this study were to quantify the phenotypic diversity in target traits to analyze the impact of breeding on these traits, and to identify genetic markers associated with traits through a genome-wide association study (GWAS). Characterization under field conditions at Nordic latitude across two years revealed a large genotypic variation and high broad-sense heritability for eleven agronomic and seed quality traits. Pairwise correlations showed that seed yield was positively correlated to plant height, number of seeds per plant, and days to maturity. Further, susceptibility to bean weevil damage was significantly higher for early flowering accessions and accessions with larger seeds. In this study, no yield penalty was found for higher seed protein content, but protein content was negatively correlated to starch content. Our results showed that while breeding advances in faba bean germplasm have resulted in increased yields and number of seeds per plant, they have also led to a selection pressure towards delayed onset of flowering and maturity. DArTseq genotyping identified 6,606 single nucleotide polymorphisms (SNPs) by alignment to the faba bean reference genome. These SNPs were used in a GWAS, revealing 51 novel SNP markers significantly associated with ten of the assessed traits. Three markers for days to flowering were found in predicted genes encoding proteins for which homologs in other plant species regulate flowering. Altogether, this work enriches the growing pool of phenotypic and genotypic data on faba bean as a valuable resource for developing efficient breeding strategies to expand crop cultivation.
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Affiliation(s)
- Hannah Ohm
- Department of Plant Breeding, Swedish University of Agricultural Sciences (SLU), Lomma, Sweden
| | - Johanna Åstrand
- Department of Plant Breeding, Swedish University of Agricultural Sciences (SLU), Lomma, Sweden
- Lantmännen Agriculture, Plant Breeding, Svalöv, Sweden
| | - Alf Ceplitis
- Lantmännen Agriculture, Plant Breeding, Svalöv, Sweden
| | | | - Cecilia Hammenhag
- Department of Plant Breeding, Swedish University of Agricultural Sciences (SLU), Lomma, Sweden
| | - Aakash Chawade
- Department of Plant Breeding, Swedish University of Agricultural Sciences (SLU), Lomma, Sweden
| | - Åsa Grimberg
- Department of Plant Breeding, Swedish University of Agricultural Sciences (SLU), Lomma, Sweden
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Johnson NA, Henderson AR, Jones JW, Beaver CE, Ahlstedt SA, Dinkins GR, Eckert NL, Endries MJ, Garner JT, Harris JL, Hartfield PD, Hubbs DW, Lane TW, McGregor MA, Moles KR, Morrison CL, Wagner MD, Williams JD, Smith CH. Glacial vicariance and secondary contact shape demographic histories in a freshwater mussel species complex. J Hered 2024; 115:72-85. [PMID: 38015800 DOI: 10.1093/jhered/esad075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 10/16/2023] [Accepted: 11/27/2023] [Indexed: 11/30/2023] Open
Abstract
Characterizing the mechanisms influencing the distribution of genetic variation in aquatic species can be difficult due to the dynamic nature of hydrological landscapes. In North America's Central Highlands, a complex history of glacial dynamics, long-term isolation, and secondary contact have shaped genetic variation in aquatic species. Although the effects of glacial history have been demonstrated in many taxa, responses are often lineage- or species-specific and driven by organismal ecology. In this study, we reconstruct the evolutionary history of a freshwater mussel species complex using a suite of mitochondrial and nuclear loci to resolve taxonomic and demographic uncertainties. Our findings do not support Pleurobema rubrum as a valid species, which is proposed for listing as threatened under the U.S. Endangered Species Act. We synonymize P. rubrum under Pleurobema sintoxia-a common and widespread species found throughout the Mississippi River Basin. Further investigation of patterns of genetic variation in P. sintoxia identified a complex demographic history, including ancestral vicariance and secondary contact, within the Eastern Highlands. We hypothesize these patterns were shaped by ancestral vicariance driven by the formation of Lake Green and subsequent secondary contact after the last glacial maximum. Our inference aligns with demographic histories observed in other aquatic taxa in the region and mirrors patterns of genetic variation of a freshwater fish species (Erimystax dissimilis) confirmed to serve as a parasitic larval host for P. sintoxia. Our findings directly link species ecology to observed patterns of genetic variation and may have significant implications for future conservation and recovery actions of freshwater mussels.
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Affiliation(s)
- Nathan A Johnson
- U.S. Geological Survey, Wetland and Aquatic Research Center, Gainesville, FL, United States
| | - Andrew R Henderson
- U.S. Fish and Wildlife Service, Ecological Services, Asheville, NC, United States
| | - Jess W Jones
- U.S. Fish and Wildlife Service, Virginia Tech University, Blacksburg, VA, United States
| | - Caitlin E Beaver
- U.S. Geological Survey, Wetland and Aquatic Research Center, Gainesville, FL, United States
| | - Steven A Ahlstedt
- McClung Museum of Natural History and Culture, University of Tennessee, Knoxville, TN, United States
| | - Gerald R Dinkins
- McClung Museum of Natural History and Culture, University of Tennessee, Knoxville, TN, United States
| | - Nathan L Eckert
- U.S. Fish and Wildlife Service, Neosho National Fish Hatchery, Neosho, MO, United States
| | - Mark J Endries
- U.S. Fish and Wildlife Service, Ecological Services, Asheville, NC, United States
| | - Jeffrey T Garner
- Alabama Division of Wildlife and Freshwater Fisheries, Florence, AL, United States
| | - John L Harris
- Arkansas State University Museum of Zoology, Jonesboro, AR, United States
| | - Paul D Hartfield
- U.S. Fish and Wildlife Service, Ecological Services, Jackson, MS, United States
| | - Don W Hubbs
- DJH Environmental Services, Camden, TN, United States
| | - Timothy W Lane
- Virginia Department of Wildlife Resources, Marion, VA, United States
| | - Monte A McGregor
- Kentucky Department of Fish and Wildlife Resources, Frankfort, KY, United States
| | - Kendall R Moles
- Arkansas Game and Fish Commission, Benton, AR, United States
| | - Cheryl L Morrison
- U.S. Geological Survey, Eastern Ecological Science Center, Kearneysville, WV, United States
| | - Matthew D Wagner
- U.S. Fish and Wildlife Service, Ecological Services, Jackson, MS, United States
| | - James D Williams
- Florida Museum, University of Florida, Gainesville, FL, United States
| | - Chase H Smith
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, United States
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5
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Niu Y, Liu Q, He Z, Raman R, Wang H, Long X, Qin H, Raman H, Parkin IAP, Bancroft I, Zou J. A Brassica carinata pan-genome platform for Brassica crop improvement. PLANT COMMUNICATIONS 2024; 5:100725. [PMID: 37803826 PMCID: PMC10811369 DOI: 10.1016/j.xplc.2023.100725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 08/21/2023] [Accepted: 09/26/2023] [Indexed: 10/08/2023]
Affiliation(s)
- Yan Niu
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Qingqing Liu
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Zhesi He
- Department of Biology, University of York, Heslington, York YO10 5DD, UK
| | - Rosy Raman
- NSW Department of Primary Industries, Wagga Wagga Agricultural Institute, Wagga Wagga, NSW 2650, Australia
| | - Hao Wang
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Xinxin Long
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Han Qin
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Harsh Raman
- NSW Department of Primary Industries, Wagga Wagga Agricultural Institute, Wagga Wagga, NSW 2650, Australia
| | - Isobel A P Parkin
- Agriculture and Agri-Food Canada, Saskatoon Research and Development Centre, Saskatoon, SK, Canada
| | - Ian Bancroft
- Department of Biology, University of York, Heslington, York YO10 5DD, UK
| | - Jun Zou
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China.
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Raman H, Raman R, Sharma N, Cui X, McVittie B, Qiu Y, Zhang Y, Hu Q, Liu S, Gororo N. Novel quantitative trait loci from an interspecific Brassica rapa derivative improve pod shatter resistance in Brassica napus. FRONTIERS IN PLANT SCIENCE 2023; 14:1233996. [PMID: 37736615 PMCID: PMC10510201 DOI: 10.3389/fpls.2023.1233996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Accepted: 07/31/2023] [Indexed: 09/23/2023]
Abstract
Pod shatter is a trait of agricultural relevance that ensures plants dehisce seeds in their native environment and has been subjected to domestication and selection for non-shattering types in several broadacre crops. However, pod shattering causes a significant yield reduction in canola (Brassica napus L.) crops. An interspecific breeding line BC95042 derived from a B. rapa/B. napus cross showed improved pod shatter resistance (up to 12-fold than a shatter-prone B. napus variety). To uncover the genetic basis and improve pod shatter resistance in new varieties, we analysed F2 and F2:3 derived populations from the cross between BC95042 and an advanced breeding line, BC95041, and genotyped with 15,498 DArTseq markers. Through genome scan, interval and inclusive composite interval mapping analyses, we identified seven quantitative trait loci (QTLs) associated with pod rupture energy, a measure for pod shatter resistance or pod strength, and they locate on A02, A03, A05, A09 and C01 chromosomes. Both parental lines contributed alleles for pod shatter resistance. We identified five pairs of significant epistatic QTLs for additive x additive, additive dominance and dominance x dominance interactions between A01/C01, A03/A07, A07/C03, A03/C03, and C01/C02 chromosomes for rupture energy. QTL effects on A03/A07 and A01/C01 were in the repulsion phase. Comparative mapping identified several candidate genes (AG, ABI3, ARF3, BP1, CEL6, FIL, FUL, GA2OX2, IND, LATE, LEUNIG, MAGL15, RPL, QRT2, RGA, SPT and TCP10) underlying main QTL and epistatic QTL interactions for pod shatter resistance. Three QTLs detected on A02, A03, and A09 were near the FUL (FRUITFULL) homologues BnaA03g39820D and BnaA09g05500D. Focusing on the FUL, we investigated putative motifs, sequence variants and the evolutionary rate of its homologues in 373 resequenced B. napus accessions of interest. BnaA09g05500D is subjected to purifying selection as it had a low Ka/Ks ratio compared to other FUL homologues in B. napus. This study provides a valuable resource for genetic improvement for yield through an understanding of the genetic mechanism controlling pod shatter resistance in Brassica species.
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Affiliation(s)
- Harsh Raman
- New South Wales (NSW) Department of Primary Industries, Wagga Wagga Agricultural Institute, Wagga Wagga, NSW, Australia
| | - Rosy Raman
- New South Wales (NSW) Department of Primary Industries, Wagga Wagga Agricultural Institute, Wagga Wagga, NSW, Australia
| | - Niharika Sharma
- New South Wales (NSW) Department of Primary Industries, Orange Agricultural Institute, Orange, NSW, Australia
| | - Xiaobo Cui
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, Hubei, China
| | - Brett McVittie
- New South Wales (NSW) Department of Primary Industries, Wagga Wagga Agricultural Institute, Wagga Wagga, NSW, Australia
| | - Yu Qiu
- New South Wales (NSW) Department of Primary Industries, Wagga Wagga Agricultural Institute, Wagga Wagga, NSW, Australia
| | - Yuanyuan Zhang
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, Hubei, China
| | - Qiong Hu
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, Hubei, China
| | - Shengyi Liu
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, Hubei, China
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Ahmad N, Fatima S, Mehmood MA, Zaman QU, Atif RM, Zhou W, Rahman MU, Gill RA. Targeted genome editing in polyploids: lessons from Brassica. FRONTIERS IN PLANT SCIENCE 2023; 14:1152468. [PMID: 37409308 PMCID: PMC10318174 DOI: 10.3389/fpls.2023.1152468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 04/11/2023] [Indexed: 07/07/2023]
Abstract
CRISPR-mediated genome editing has emerged as a powerful tool for creating targeted mutations in the genome for various applications, including studying gene functions, engineering resilience against biotic and abiotic stresses, and increasing yield and quality. However, its utilization is limited to model crops for which well-annotated genome sequences are available. Many crops of dietary and economic importance, such as wheat, cotton, rapeseed-mustard, and potato, are polyploids with complex genomes. Therefore, progress in these crops has been hampered due to genome complexity. Excellent work has been conducted on some species of Brassica for its improvement through genome editing. Although excellent work has been conducted on some species of Brassica for genome improvement through editing, work on polyploid crops, including U's triangle species, holds numerous implications for improving other polyploid crops. In this review, we summarize key examples from genome editing work done on Brassica and discuss important considerations for deploying CRISPR-mediated genome editing more efficiently in other polyploid crops for improvement.
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Affiliation(s)
- Niaz Ahmad
- National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, Pakistan
| | - Samia Fatima
- National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, Pakistan
| | - Muhammad Aamer Mehmood
- Department of Bioinformatics & Biotechnology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Qamar U. Zaman
- Hainan Yazhou Bay Seed Laboratory, Sanya Nanfan Research Institute of Hainan University, Sanya, China
- College of Tropical Crops, Hainan University, Haikou, China
| | - Rana Muhammad Atif
- National Center of Genome Editing, Center of Advanced Studies, Agriculture and Food Security, University of Agriculture, Faisalabad, Pakistan
- Department of Plant Breeding and Genetics, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Weijun Zhou
- Ministry of Agriculture and Rural Affairs Key Lab of Spectroscopy Sensing, Institute of Crop Science, Zhejiang University, Hangzhou, China
| | - Mehboob-ur Rahman
- National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, Pakistan
| | - Rafaqat Ali Gill
- Key Laboratory for Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
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8
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Dossa EN, Shimelis H, Mrema E, Shayanowako ATI, Laing M. Genetic resources and breeding of maize for Striga resistance: a review. FRONTIERS IN PLANT SCIENCE 2023; 14:1163785. [PMID: 37235028 PMCID: PMC10206272 DOI: 10.3389/fpls.2023.1163785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Accepted: 04/07/2023] [Indexed: 05/28/2023]
Abstract
The potential yield of maize (Zea mays L.) and other major crops is curtailed by several biotic, abiotic, and socio-economic constraints. Parasitic weeds, Striga spp., are major constraints to cereal and legume crop production in sub-Saharan Africa (SSA). Yield losses reaching 100% are reported in maize under severe Striga infestation. Breeding for Striga resistance has been shown to be the most economical, feasible, and sustainable approach for resource-poor farmers and for being environmentally friendly. Knowledge of the genetic and genomic resources and components of Striga resistance is vital to guide genetic analysis and precision breeding of maize varieties with desirable product profiles under Striga infestation. This review aims to present the genetic and genomic resources, research progress, and opportunities in the genetic analysis of Striga resistance and yield components in maize for breeding. The paper outlines the vital genetic resources of maize for Striga resistance, including landraces, wild relatives, mutants, and synthetic varieties, followed by breeding technologies and genomic resources. Integrating conventional breeding, mutation breeding, and genomic-assisted breeding [i.e., marker-assisted selection, quantitative trait loci (QTL) analysis, next-generation sequencing, and genome editing] will enhance genetic gains in Striga resistance breeding programs. This review may guide new variety designs for Striga-resistance and desirable product profiles in maize.
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Affiliation(s)
- Emeline Nanou Dossa
- School of Agricultural, Earth and Environmental Sciences, University of KwaZulu-Natal, Pietermaritzburg, South Africa
| | - Hussein Shimelis
- School of Agricultural, Earth and Environmental Sciences, University of KwaZulu-Natal, Pietermaritzburg, South Africa
| | - Emmanuel Mrema
- School of Agricultural, Earth and Environmental Sciences, University of KwaZulu-Natal, Pietermaritzburg, South Africa
- Tanzania Agricultural Research Institute, Tumbi Center, Tabora, Tanzania
| | | | - Mark Laing
- School of Agricultural, Earth and Environmental Sciences, University of KwaZulu-Natal, Pietermaritzburg, South Africa
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9
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Zhang Y, Zhang Q, Wang H, Tao S, Cao H, Shi Y, Bakirov A, Xu A, Huang Z. Discovery of common loci and candidate genes for controlling salt-alkali tolerance and yield-related traits in Brassica napus L. PLANT CELL REPORTS 2023; 42:1039-1057. [PMID: 37076701 DOI: 10.1007/s00299-023-03011-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Accepted: 03/27/2023] [Indexed: 05/03/2023]
Abstract
KEY MESSAGE Common loci and candidate genes for controlling salt-alkali tolerance and yield-related traits were identified in Brassica napus combining QTL mapping with transcriptome under salt and alkaline stresses. The yield of rapeseed (Brassica napus L.) is determined by multiple yield-related traits, which are susceptible to environmental factors. Many yield-related quantitative trait loci (QTLs) have been reported in Brassica napus; however, no studies have been conducted to investigate both salt-alkali tolerance and yield-related traits simultaneously. Here, specific-locus amplified fragment sequencing (SLAF-seq) technologies were utilized to map the QTLs for salt-alkali tolerance and yield-related traits. A total of 65 QTLs were identified, including 30 QTLs for salt-alkali tolerance traits and 35 QTLs for yield-related traits, accounting for 7.61-27.84% of the total phenotypic variations. Among these QTLs, 18 unique QTLs controlling two to four traits were identified by meta-analysis. Six novel and unique QTLs were detected for salt-alkali tolerance traits. By comparing these unique QTLs for salt-alkali tolerance traits with those previously reported QTLs for yield-related traits, seven co-localized chromosomal regions were identified on A09 and A10. Combining QTL mapping with transcriptome of two parents under salt and alkaline stresses, thirteen genes were identified as the candidates controlling both salt-alkali tolerance and yield. These findings provide useful information for future breeding of high-yield cultivars resistant to alkaline and salt stresses.
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Affiliation(s)
- Yan Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Qi Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Han Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Shunxian Tao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Hanming Cao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Yiji Shi
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Aldiyar Bakirov
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Aixia Xu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Zhen Huang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China.
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Odesola KA, Olawuyi OJ, Paliwal R, Oyatomi OA, Abberton MT. Genome-Wide association analysis of phenotypic traits in Bambara groundnut under drought-stressed and non-stressed conditions based on DArTseq SNP. FRONTIERS IN PLANT SCIENCE 2023; 14:1104417. [PMID: 36866383 PMCID: PMC9972976 DOI: 10.3389/fpls.2023.1104417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 01/05/2023] [Indexed: 06/18/2023]
Abstract
INTRODUCTION Bambara groundnut (BG) (Vigna subterranea [L.] Verdc) is an indigenous, resilient, but underutilized leguminous crop that occurs mostly as genetically heterogeneous landraces with limited information on the drought tolerant attributes. This study elucidates the associations between sequencing-based diversity array technology (DArTseq) and phenotypic character as well as differing indices related to drought tolerance in one hundred accessions of Bambara groundnut. METHODS The field experiments were conducted at IITA research stations in Kano and Ibadan between 2016 and 2018 planting seasons. The experiments were arranged in randomised complete block design with three replications, under the different water regimes. The phenotypic traits evaluated was further to construct the dendrogram. Genome-wide association mapping was conducted based on 5927 DArTs loci with < 20% missing data. RESULTS AND DISCUSSIONS The genome wide association study predicted drought tolerance in Bambara accessions for geometric mean productivity (GMP) and stress tolerance index (STI). TVSu-423 had the highest GMP and STI values (28.50, 2.40), while TVSu-2017 had the lowest at GMP (1.74) and STI (0.01) respectively. The relative water content (%) was significantly higher for accessions; TVSu-266 (60.35, 61.49), TVSu-2 (58.29, 53.94), and TVSu-411 (55.17, 58.92) in 2016/2017 and 2017/2018, respectively. The phenotypic characters studied delineated the accessions into two major clusters and five distinct sub-clusters, indicating variations across all the geographical locations. The 5,927 DArTseq genomic markers in association with STI further grouped the 100 accessions into two main clusters. TVSu-1897 from Botswana (Southern Africa) was in the first cluster, while the remaining 99 accessions from Western, Central, and Eastern Africa made up the second cluster. The eight significant Quantitative Trait Loci (QTLs) (24346377|F|0-22:A>G-22:A>G, 24384105|F|0-56:A>G33 :A> G, 24385643|F|0-53:G>C-53:G>C, 24385696|F|0-43:A>G-43:A>G, 4177257|F|0-44:A>T-44:A>T, 4182070|F|0-66:G>A-66:G>A, 4183483|F|0-24:G>A-24:G>A, 4183904|F|0-11:C>T-11:C>T) identified with Bonferroni threshold was in association with STI, indicative of variations under the drought-stressed condition. The observation of consistent SNPs in the 2016 and 2017 planting seasons, as well as in combination with the 2016 and 2017 planting seasons, led to the designation of these QTLs as significant. The drought selected accessions could form basis for hybridization breeding. The identified quantitative trait loci could be useful in marker-assisted selection in drought molecular breeding programs.
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Affiliation(s)
- Kafilat Abiodun Odesola
- Department of Biological Sciences, Bells University of Technology, Sango Otta, Ogun State, Nigeria
- Genetic Resources Centre, International Institute of Tropical Agriculture, Ibadan, Oyo State, Nigeria
- Department of Botany, University of Ibadan, Ibadan, Oyo State, Nigeria
| | | | - Rajneesh Paliwal
- Genetic Resources Centre, International Institute of Tropical Agriculture, Ibadan, Oyo State, Nigeria
| | - Olaniyi Ajewole Oyatomi
- Genetic Resources Centre, International Institute of Tropical Agriculture, Ibadan, Oyo State, Nigeria
| | - Michael T. Abberton
- Genetic Resources Centre, International Institute of Tropical Agriculture, Ibadan, Oyo State, Nigeria
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Cantila AY, Thomas WJ, Saad NSM, Severn-Ellis AA, Anderson R, Bayer PE, Edwards D, Van de Wouw AP, Batley J. Identification of candidate genes for LepR1 resistance against Leptosphaeria maculans in Brassica napus. FRONTIERS IN PLANT SCIENCE 2023; 14:1051994. [PMID: 36866377 PMCID: PMC9971972 DOI: 10.3389/fpls.2023.1051994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 01/19/2023] [Indexed: 06/18/2023]
Abstract
Utilising resistance (R) genes, such as LepR1, against Leptosphaeria maculans, the causal agent of blackleg in canola (Brassica napus), could help manage the disease in the field and increase crop yield. Here we present a genome wide association study (GWAS) in B. napus to identify LepR1 candidate genes. Disease phenotyping of 104 B. napus genotypes revealed 30 resistant and 74 susceptible lines. Whole genome re-sequencing of these cultivars yielded over 3 million high quality single nucleotide polymorphisms (SNPs). GWAS in mixed linear model (MLM) revealed a total of 2,166 significant SNPs associated with LepR1 resistance. Of these SNPs, 2108 (97%) were found on chromosome A02 of B. napus cv. Darmor bzh v9 with a delineated LepR1_mlm1 QTL at 15.11-26.08 Mb. In LepR1_mlm1, there are 30 resistance gene analogs (RGAs) (13 nucleotide-binding site-leucine rich repeats (NLRs), 12 receptor-like kinases (RLKs), and 5 transmembrane-coiled-coil (TM-CCs)). Sequence analysis of alleles in resistant and susceptible lines was undertaken to identify candidate genes. This research provides insights into blackleg resistance in B. napus and assists identification of the functional LepR1 blackleg resistance gene.
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Affiliation(s)
- Aldrin Y. Cantila
- School of Biological Sciences, The University of Western Australia, Crawley, WA, Australia
| | - William J.W. Thomas
- School of Biological Sciences, The University of Western Australia, Crawley, WA, Australia
| | - Nur Shuhadah Mohd Saad
- School of Biological Sciences, The University of Western Australia, Crawley, WA, Australia
| | - Anita A. Severn-Ellis
- School of Biological Sciences, The University of Western Australia, Crawley, WA, Australia
| | - Robyn Anderson
- School of Biological Sciences, The University of Western Australia, Crawley, WA, Australia
| | - Philipp E. Bayer
- School of Biological Sciences, The University of Western Australia, Crawley, WA, Australia
| | - David Edwards
- School of Biological Sciences, The University of Western Australia, Crawley, WA, Australia
| | | | - Jacqueline Batley
- School of Biological Sciences, The University of Western Australia, Crawley, WA, Australia
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Frère CH, O'Reilly GD, Strickland K, Schultz A, Hohwieler K, Hanger J, de Villiers D, Cristescu R, Powell D, Sherwin W. Evaluating the genetic consequences of population subdivision as it unfolds and how to best mitigate them: A rare story about koalas. Mol Ecol 2023; 32:2174-2185. [PMID: 36756702 DOI: 10.1111/mec.16877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Revised: 01/23/2023] [Accepted: 01/25/2023] [Indexed: 02/10/2023]
Abstract
The genetic consequences of the subdivision of populations are regarded as significant to long-term evolution, and research has shown that the scale and speed at which this is now occurring is critically reducing the adaptive potential of most species which inhabit human-impacted landscapes. Here, we provide a rare and, to our knowledge, the first analysis of this process while it is happening and demonstrate a method of evaluating the effect of mitigation measures such as fauna crossings. We did this by using an extensive genetic data set collected from a koala population which was intensely monitored during the construction of linear transport infrastructure which resulted in the subdivision of their population. First, we found that both allelic richness and effective population size decreased through the process of population subdivision. Second, we predicted the extent to which genetic drift could impact genetic diversity over time and showed that after only 10 generations the resulting two subdivided populations could experience between 12% and 69% loss in genetic diversity. Lastly, using forward simulations we estimated that a minimum of eight koalas would need to disperse from each side of the subdivision per generation to maintain genetic connectivity close to zero but that 16 koalas would ensure that both genetic connectivity and diversity remained unchanged. These results have important consequences for the genetic management of species in human-impacted landscapes by showing which genetic metrics are best to identify immediate loss in genetic diversity and how to evaluate the effectiveness of any mitigation measures.
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Affiliation(s)
- C H Frère
- School of Biological Sciences, University of Queensland, St Lucia, Queensland, Australia
| | - G D O'Reilly
- The School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - K Strickland
- Institute of Ecology and Evolution, University of Edinburgh, Edinburgh, UK
| | - A Schultz
- Icelandic Museum of Natural History (Náttúruminjasafn Íslands), Reykjavik, Iceland
| | - K Hohwieler
- School of Science, Technology and Engineering, University of the Sunshine Coast, Queensland, Australia
| | - J Hanger
- Endeavour Veterinary Ecology Pty Ltd, Toorbul, Queensland, Australia
| | - D de Villiers
- Endeavour Veterinary Ecology Pty Ltd, Toorbul, Queensland, Australia
| | - R Cristescu
- School of Science, Technology and Engineering, University of the Sunshine Coast, Queensland, Australia
| | - D Powell
- School of Science, Technology and Engineering, University of the Sunshine Coast, Queensland, Australia
| | - W Sherwin
- The School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
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Du H, Raman H, Kawasaki A, Perera G, Diffey S, Snowdon R, Raman R, Ryan PR. A genome-wide association study (GWAS) identifies multiple loci linked with the natural variation for Al 3+ resistance in Brassica napus. FUNCTIONAL PLANT BIOLOGY : FPB 2022; 49:845-860. [PMID: 35753342 DOI: 10.1071/fp22073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 05/28/2022] [Indexed: 06/15/2023]
Abstract
Acid soils limit yields of many important crops including canola (Brassica napus ), Australia's third largest crop. Aluminium (Al3+ ) stress is the main cause of this limitation primarily because the toxic Al3+ present inhibits root growth. Breeding programmes do not target acid-soil tolerance in B. napus because genetic variation and convincing quantitative trait loci have not been reported. We conducted a genome-wide association study (GWAS) using the BnASSYST diversity panel of B. napus genotyped with 35 729 high-quality DArTseq markers. We screened 352 B. napus accessions in hydroponics with and without a toxic concentration of AlCl3 (12μM, pH 4.3) for 12days and measured shoot biomass, root biomass, and root length. By accounting for both population structure and kinship matrices, five significant quantitative trait loci for different measures of resistance were identified using incremental Al3+ resistance indices. Within these quantitative trait locus regions of B. napus , 40 Arabidopsis thaliana gene orthologues were identified, including some previously linked with Al3+ resistance. GWAS analysis indicated that multiple genes are responsible for the natural variation in Al3+ resistance in B. napus . The results provide new genetic resources and markers to enhance that Al3+ resistance of B. napus germplasm via genomic and marker-assisted selection.
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Affiliation(s)
- Hanmei Du
- CSIRO Agriculture and Food, Canberra, ACT 2601, Australia; and Key Laboratory of Biology and Genetic Improvement of Maize in Southwest China, Maize Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Harsh Raman
- NSW Department of Primary Industries, Wagga Wagga, NSW 2650, Australia
| | - Akitomo Kawasaki
- CSIRO Agriculture and Food, Canberra, ACT 2601, Australia; and NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Advanced Gene Technology Centre, Menangle, NSW 2568, Australia
| | - Geetha Perera
- CSIRO Agriculture and Food, Canberra, ACT 2601, Australia
| | | | - Rod Snowdon
- Justus Liebig University, Department of Plant Breeding Institute, Giessen 35391, Germany
| | - Rosy Raman
- NSW Department of Primary Industries, Wagga Wagga, NSW 2650, Australia
| | - Peter R Ryan
- CSIRO Agriculture and Food, Canberra, ACT 2601, Australia
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14
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Afridi M, Ahmad K, Malik SS, Rehman N, Yasin M, Khan SM, Hussain A, Khan MR. Genome-wide identification, phylogeny, and expression profiling analysis of shattering genes in rapeseed and mustard plants. J Genet Eng Biotechnol 2022; 20:124. [PMID: 35980545 PMCID: PMC9388710 DOI: 10.1186/s43141-022-00408-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 08/05/2022] [Indexed: 11/22/2022]
Abstract
Background Non-synchronized pods shattering in the Brassicaceae family bring upon huge yield losses around the world. The shattering process was validated to be controlled by eight genes in Arabidopsis, including SHP1, SHP2, FUL, IND, ALC, NAC, RPL, and PG. We performed genome-wide identification, characterization, and expression analysis of shattering genes in B.napus and B. juncea to gain understanding into this gene family and to explain their expression patterns in fresh and mature siliques. Results A comprehensive genome investigation of B.napus and B.juncea revealed 32 shattering genes, which were identified and categorized using protein motif structure, exon-intron organization, and phylogeny. The phylogenetic study revealed that these shattering genes contain little duplications, determined with a distinct chromosome number. Motifs of 32 shattering proteins were observed where motifs1 and 2 were found to be more conserved. A single motif was observed for other genes like Br-nS7, Br-nS9, Br-nS10, Br-jS21, Br-jS23, Br-jS24, Br-jS25, and Br-jS26. Synteny analysis was performed that validated a conserved pattern of blocks among these cultivars. RT-PCR based expressions profiles showed higher expression of shattering genes in B. juncea as compared to B.napus. SHP1, SHP2, and FUL gene were expressed more in mature silique. ALC gene was upregulated in fresh silique of B. napus but downregulation of ALC were observed in fresh silique of B. juncea. Conclusion This study authenticates the presence of shattering genes in the local cultivars of Brassica. It has been validated that the expression of shattering genes were more in B. juncea as compared to B.napus. The outcomes of this study contribute to the screening of more candidate genes for further investigation.
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Affiliation(s)
- Mahideen Afridi
- National Centre for Bioinformatics, Quaid-I-Azam University, Islamabad, 45320, Pakistan.
| | - Khurshid Ahmad
- Department of Biological Sciences, International Islamic University, Islamabad, 44000, Pakistan
| | - Shahana Seher Malik
- Department of Biology, College of Science, United Arab Emirates University, 15551, Al Ain, United Arab Emirates
| | - Nazia Rehman
- National Institute for Genomics and Advanced Biotechnology, National Agricultural Research Center, Park Road, Islamabad, 44000, Pakistan
| | - Muhammad Yasin
- National Centre for Bioinformatics, Quaid-I-Azam University, Islamabad, 45320, Pakistan
| | - Shujaul Mulk Khan
- Department of Plant Sciences, Quaid-I-Azam University, Islamabad, 45320, Pakistan
| | - Adil Hussain
- Food and Biotechnology Research Centre (FBRC), Pakistan Council of Scientific and Industrial Research (PCSIR) Laboratories Complex, Ferozepur Road, Lahore, Punjab, 56400, Pakistan
| | - Muhammad Ramzan Khan
- National Centre for Bioinformatics, Quaid-I-Azam University, Islamabad, 45320, Pakistan.,National Institute for Genomics and Advanced Biotechnology, National Agricultural Research Center, Park Road, Islamabad, 44000, Pakistan
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15
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Rajendran NR, Qureshi N, Pourkheirandish M. Genotyping by Sequencing Advancements in Barley. FRONTIERS IN PLANT SCIENCE 2022; 13:931423. [PMID: 36003814 PMCID: PMC9394214 DOI: 10.3389/fpls.2022.931423] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 06/20/2022] [Indexed: 06/15/2023]
Abstract
Barley is considered an ideal crop to study cereal genetics due to its close relationship with wheat and diploid ancestral genome. It plays a crucial role in reducing risks to global food security posed by climate change. Genetic variations in the traits of interest in crops are vital for their improvement. DNA markers have been widely used to estimate these variations in populations. With the advancements in next-generation sequencing, breeders could access different types of genetic variations within different lines, with single-nucleotide polymorphisms (SNPs) being the most common type. However, genotyping barley with whole genome sequencing (WGS) is challenged by the higher cost and computational demand caused by the large genome size (5.5GB) and a high proportion of repetitive sequences (80%). Genotyping-by-sequencing (GBS) protocols based on restriction enzymes and target enrichment allow a cost-effective SNP discovery by reducing the genome complexity. In general, GBS has opened up new horizons for plant breeding and genetics. Though considered a reliable alternative to WGS, GBS also presents various computational difficulties, but GBS-specific pipelines are designed to overcome these challenges. Moreover, a robust design for GBS can facilitate the imputation to the WGS level of crops with high linkage disequilibrium. The complete exploitation of GBS advancements will pave the way to a better understanding of crop genetics and offer opportunities for the successful improvement of barley and its close relatives.
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Affiliation(s)
- Nirmal Raj Rajendran
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, VIC, Australia
| | - Naeela Qureshi
- International Maize and Wheat Improvement Center (CIMMYT), El Batan, Texcoco, Estado de Mexico, Mexico
| | - Mohammad Pourkheirandish
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, VIC, Australia
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Raman H, Raman R, Pirathiban R, McVittie B, Sharma N, Liu S, Qiu Y, Zhu A, Kilian A, Cullis B, Farquhar GD, Stuart‐Williams H, White R, Tabah D, Easton A, Zhang Y. Multienvironment QTL analysis delineates a major locus associated with homoeologous exchanges for water-use efficiency and seed yield in canola. PLANT, CELL & ENVIRONMENT 2022; 45:2019-2036. [PMID: 35445756 PMCID: PMC9325393 DOI: 10.1111/pce.14337] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 04/06/2022] [Indexed: 05/29/2023]
Abstract
Canola varieties exhibit variation in drought avoidance and drought escape traits, reflecting adaptation to water-deficit environments. Our understanding of underlying genes and their interaction across environments in improving crop productivity is limited. A doubled haploid population was analysed to identify quantitative trait loci (QTL) associated with water-use efficiency (WUE) related traits. High WUE in the vegetative phase was associated with low seed yield. Based on the resequenced parental genome data, we developed sequence-capture-based markers and validated their linkage with carbon isotope discrimination (Δ13 C) in an F2 population. RNA sequencing was performed to determine the expression of candidate genes underlying Δ13 C QTL. QTL contributing to main and QTL × environment interaction effects for Δ13 C and yield were identified. One multiple-trait QTL for Δ13 C, days to flower, plant height, and seed yield was identified on chromosome A09. Interestingly, this QTL region overlapped with a homoeologous exchange (HE) event, suggesting its association with the multiple traits. Transcriptome analysis revealed 121 significantly differentially expressed genes underlying Δ13 C QTL on A09 and C09, including in HE regions. Sorting out the negative relationship between vegetative WUE and seed yield is a priority. Genetic and genomic resources and knowledge so developed could improve canola WUE and yield.
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Affiliation(s)
- Harsh Raman
- NSW Department of Primary IndustriesWagga Wagga Agricultural InstituteWagga WaggaNew South WalesAustralia
| | - Rosy Raman
- NSW Department of Primary IndustriesWagga Wagga Agricultural InstituteWagga WaggaNew South WalesAustralia
| | - Ramethaa Pirathiban
- Centre for Biometrics and Data Science for Sustainable Primary Industries, National Institute for Applied Statistics Research AustraliaUniversity of WollongongWollongongNew South WalesAustralia
| | - Brett McVittie
- NSW Department of Primary IndustriesWagga Wagga Agricultural InstituteWagga WaggaNew South WalesAustralia
| | - Niharika Sharma
- NSW Department of Primary IndustriesOrange Agricultural InstituteOrangeNew South WalesAustralia
| | - Shengyi Liu
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs of PRCOil Crops Research Institute, Chinese Academy of Agricultural SciencesWuhanHubeiChina
| | - Yu Qiu
- NSW Department of Primary IndustriesWagga Wagga Agricultural InstituteWagga WaggaNew South WalesAustralia
| | - Anyu Zhu
- Diversity Arrays Technology P/LUniversity of CanberraCanberraAustralian Capital TerritoryAustralia
| | - Andrzej Kilian
- Diversity Arrays Technology P/LUniversity of CanberraCanberraAustralian Capital TerritoryAustralia
| | - Brian Cullis
- Centre for Biometrics and Data Science for Sustainable Primary Industries, National Institute for Applied Statistics Research AustraliaUniversity of WollongongWollongongNew South WalesAustralia
| | - Graham D. Farquhar
- Research School of BiologyAustralian National UniversityCanberraAustralian Capital TerritoryAustralia
| | - Hilary Stuart‐Williams
- Research School of BiologyAustralian National UniversityCanberraAustralian Capital TerritoryAustralia
| | | | - David Tabah
- Advanta Seeds Pty LtdToowoombaQueenslandAustralia
| | | | - Yuanyuan Zhang
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs of PRCOil Crops Research Institute, Chinese Academy of Agricultural SciencesWuhanHubeiChina
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Zhang P, Lan C, Singh RP, Huerta-Espino J, Li Z, Lagudah E, Bhavani S. Identification and Characterization of Resistance Loci to Wheat Leaf Rust and Stripe Rust in Afghan Landrace "KU3067". FRONTIERS IN PLANT SCIENCE 2022; 13:894528. [PMID: 35837449 PMCID: PMC9274257 DOI: 10.3389/fpls.2022.894528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 04/25/2022] [Indexed: 06/15/2023]
Abstract
Leaf rust and stripe rust are important wheat diseases worldwide causing significant losses where susceptible varieties are grown. Resistant cultivars offer long-term control and reduce the use of hazardous chemicals, which can be detrimental to both human health and the environment. Land races have been a valuable resource for mining new genes for various abiotic and biotic stresses including wheat rusts. Afghan wheat landrace "KU3067" displayed high seedling infection type (IT) for leaf rust and low IT for stripe rust; however, it displayed high levels of field resistance for both rusts when tested for multiple seasons against the Mexican rust isolates. This study focused on identifying loci-conferring seedling resistance to stripe rust, and also loci-conferring adult plant resistance (APR) against the Mexican races of leaf rust and stripe rust. A backcrossed inbred line (BIL) population advanced to the BC1F5 generation derived from the cross of KU3067 and Apav (triple rust susceptible line) was used for both, inheritance and QTL mapping studies. The population and parents were genotyped with Diversity Arrays Technology-genotyping-by-sequencing (DArT-Seq) and phenotyped for leaf rust and stripe rust response at both seedling and adult plant stages during multiple seasons in Mexico with relevant pathotypes. Mapping results identified an all-stage resistance gene for stripe rust, temporarily designated as YrKU, on chromosome 7BL. In total, six QTL-conferring APR to leaf rust on 1AS, 2AL, 4DL, 6BL, 7AL, and 7BL, and four QTL for stripe rust resistance on 1BS, 2AL, 4DL, and 7BL were detected in the analyses. Among these, pleiotropic gene Lr67/Yr46 on 4DL with a significantly large effect is the first report in an Afghan landrace-conferring resistance to both leaf and stripe rusts. QLr.cim-7BL/YrKU showed pleiotropic resistance to both rusts and explained 7.5-17.2 and 12.6-19.3% of the phenotypic variance for leaf and stripe rusts, respectively. QYr.cim-1BS and QYr.cim-2AL detected in all stripe environments with phenotypic variance explained (PVE) 12.9-20.5 and 5.4-12.5%, and QLr.cim-6BL are likely to be new. These QTL and their closely linked markers will be useful for fine mapping and marker-assisted selection (MAS) in breeding for durable resistance to multiple rust diseases.
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Affiliation(s)
- Peipei Zhang
- State Key Laboratory of North China Crop Improvement and Regulation, College of Plant Protection, Hebei Agricultural University, Baoding, China
| | - Caixia Lan
- Hubei Hongshan Laboratory, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, China
| | - Ravi P. Singh
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | - Julio Huerta-Espino
- Campo Experimental Valle de México the National Institute of Forestry, Agricultural and Livestock Research (INIFAP), Texcoco, Mexico
| | - Zaifeng Li
- State Key Laboratory of North China Crop Improvement and Regulation, College of Plant Protection, Hebei Agricultural University, Baoding, China
| | - Evans Lagudah
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Plant Industry, Canberra, ACT, Australia
| | - Sridhar Bhavani
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
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Alemu A, Brantestam AK, Chawade A. Unraveling the Genetic Basis of Key Agronomic Traits of Wrinkled Vining Pea ( Pisum sativum L.) for Sustainable Production. FRONTIERS IN PLANT SCIENCE 2022; 13:844450. [PMID: 35360298 PMCID: PMC8964273 DOI: 10.3389/fpls.2022.844450] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 02/14/2022] [Indexed: 06/14/2023]
Abstract
Estimating the allelic variation and exploring the genetic basis of quantitatively inherited complex traits are the two foremost breeding scenarios for sustainable crop production. The current study utilized 188 wrinkled vining pea genotypes comprising historical varieties and breeding lines to evaluate the existing genetic diversity and to detect molecular markers associated with traits relevant to vining pea production, such as wrinkled vining pea yield (YTM100), plant height (PH), earliness (ERL), adult plant resistance to downy mildew (DM), pod length (PDL), numbers of pods per plant (PDP), number of peas per pod (PPD), and percent of small wrinkled vining peas (PSP). Marker-trait associations (MTAs) were conducted using 6902 quality single nucleotide polymorphism (SNP) markers generated from the diversity arrays technology sequencing (DArTseq) and Genotyping-by-sequencing (GBS) sequencing methods. The best linear unbiased prediction (BLUP) values were estimated from the two-decades-long (1999-2020) unbalanced phenotypic data sets recorded from two private breeding programs, the Findus and the Birds eye, now owned by Nomad Foods. Analysis of variance revealed a highly significant variation between genotypes and genotype-by-environment interactions for the ten traits. The genetic diversity and population structure analyses estimated an intermediate level of genetic variation with two optimal sub-groups within the current panel. A total of 48 significant (P < 0.0001) MTAs were identified for eight different traits, including five for wrinkled vining pea yield on chr2LG1, chr4LG4, chr7LG7, and scaffolds (two), and six for adult plant resistance to downy mildew on chr1LG6, chr3LG5 (two), chr6LG2, and chr7LG7 (two). We reported several novel MTAs for different crucial traits with agronomic importance in wrinkled vining pea production for the first time, and these candidate markers could be easily validated and integrated into the active breeding programs for marker-assisted selection.
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Affiliation(s)
- Admas Alemu
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | | | - Aakash Chawade
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
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Tandayu E, Borpatragohain P, Mauleon R, Kretzschmar T. Genome-Wide Association Reveals Trait Loci for Seed Glucosinolate Accumulation in Indian Mustard ( Brassica juncea L.). PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11030364. [PMID: 35161346 PMCID: PMC8838242 DOI: 10.3390/plants11030364] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/18/2022] [Accepted: 01/26/2022] [Indexed: 05/05/2023]
Abstract
Glucosinolates (GSLs) are sulphur- and nitrogen-containing secondary metabolites implicated in the fitness of Brassicaceae and appreciated for their pungency and health-conferring properties. In Indian mustard (Brassica juncea L.), GSL content and composition are seed-quality-determining traits affecting its economic value. Depending on the end use, i.e., condiment or oil, different GSL levels constitute breeding targets. The genetic control of GSL accumulation in Indian mustard, however, is poorly understood, and current knowledge of GSL biosynthesis and regulation is largely based on Arabidopsis thaliana. A genome-wide association study was carried out to dissect the genetic architecture of total GSL content and the content of two major GSLs, sinigrin and gluconapin, in a diverse panel of 158 Indian mustard lines, which broadly grouped into a South Asia cluster and outside-South-Asia cluster. Using 14,125 single-nucleotide polymorphisms (SNPs) as genotyping input, seven distinct significant associations were discovered for total GSL content, eight associations for sinigrin content and 19 for gluconapin. Close homologues of known GSL structural and regulatory genes were identified as candidate genes in proximity to peak SNPs. Our results provide a comprehensive map of the genetic control of GLS biosynthesis in Indian mustard, including priority targets for further investigation and molecular marker development.
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Raman R, Warren A, Krysinska-Kaczmarek M, Rohan M, Sharma N, Dron N, Davidson J, Moore K, Hobson K. Genome-Wide Association Analyses Track Genomic Regions for Resistance to Ascochyta rabiei in Australian Chickpea Breeding Germplasm. FRONTIERS IN PLANT SCIENCE 2022; 13:877266. [PMID: 35665159 PMCID: PMC9159299 DOI: 10.3389/fpls.2022.877266] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 04/08/2022] [Indexed: 05/05/2023]
Abstract
Ascochyta blight (AB), caused by a necrotrophic fungus, Ascochyta rabiei (syn. Phoma rabiei) has the potential to destroy the chickpea industry worldwide, due to limited sources of genetic resistance in the cultivated gene pool, high evolutionary potential of the pathogen and challenges with integrated disease management. Therefore, the deployment of stable genetic resistance in new cultivars could provide an effective disease control strategy. To investigate the genetic basis of AB resistance, genotyping-by-sequencing based DArTseq-single nucleotide polymorphism (SNP) marker data along with phenotypic data of 251 advanced breeding lines and chickpea cultivars were used to perform genome-wide association (GWAS) analysis. Host resistance was evaluated seven weeks after sowing using two highly aggressive single spore isolates (F17191-1 and TR9571) of A. rabiei. GWAS analyses based on single-locus and multi-locus mixed models and haplotyping trend regression identified twenty-six genomic regions on Ca1, Ca4, and Ca6 that showed significant association with resistance to AB. Two haplotype blocks (HB) on chromosome Ca1; HB5 (992178-1108145 bp), and HB8 (1886221-1976301 bp) were associated with resistance against both isolates. Nine HB on the chromosome, Ca4, spanning a large genomic region (14.9-56.6 Mbp) were also associated with resistance, confirming the role of this chromosome in providing resistance to AB. Furthermore, trait-marker associations in two F3 derived populations for resistance to TR9571 isolate at the seedling stage under glasshouse conditions were also validated. Eighty-nine significantly associated SNPs were located within candidate genes, including genes encoding for serine/threonine-protein kinase, Myb protein, quinone oxidoreductase, and calmodulin-binding protein all of which are implicated in disease resistance. Taken together, this study identifies valuable sources of genetic resistance, SNP markers and candidate genes underlying genomic regions associated with AB resistance which may enable chickpea breeding programs to make genetic gains via marker-assisted/genomic selection strategies.
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Affiliation(s)
- Rosy Raman
- NSW Department of Primary Industries, Wagga Wagga Agricultural Institute, Wagga Wagga, NSW, Australia
- *Correspondence: Rosy Raman,
| | - Annie Warren
- NSW Department of Primary Industries, Tamworth Agricultural Institute, Tamworth, NSW, Australia
| | | | - Maheswaran Rohan
- NSW Department of Primary Industries, Wagga Wagga Agricultural Institute, Wagga Wagga, NSW, Australia
| | - Niharika Sharma
- NSW Department of Primary Industries, Orange Agricultural Institute, Orange, NSW, Australia
| | - Nicole Dron
- NSW Department of Primary Industries, Tamworth Agricultural Institute, Tamworth, NSW, Australia
| | - Jenny Davidson
- South Australian Research and Development Institute, Urrbrae, SA, Australia
| | - Kevin Moore
- NSW Department of Primary Industries, Tamworth Agricultural Institute, Tamworth, NSW, Australia
| | - Kristy Hobson
- NSW Department of Primary Industries, Tamworth Agricultural Institute, Tamworth, NSW, Australia
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21
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Yashiro T, Tea YK, Van Der Wal C, Nozaki T, Mizumoto N, Hellemans S, Matsuura K, Lo N. Enhanced heterozygosity from male meiotic chromosome chains is superseded by hybrid female asexuality in termites. Proc Natl Acad Sci U S A 2021; 118:e2009533118. [PMID: 34903643 PMCID: PMC8713478 DOI: 10.1073/pnas.2009533118] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/02/2021] [Indexed: 11/18/2022] Open
Abstract
Although males are a ubiquitous feature of animals, they have been lost repeatedly in diverse lineages. The tendency for obligate asexuality to evolve is thought to be reduced in animals whose males play a critical role beyond the contribution of gametes, for example, via care of offspring or provision of nuptial gifts. To our knowledge, the evolution of obligate asexuality in such species is unknown. In some species that undergo frequent inbreeding, males are hypothesized to play a key role in maintaining genetic heterozygosity through the possession of neo-sex chromosomes, although empirical evidence for this is lacking. Because inbreeding is a key feature of the life cycle of termites, we investigated the potential role of males in promoting heterozygosity within populations through karyotyping and genome-wide single-nucleotide polymorphism analyses of the drywood termite Glyptotermes nakajimai We showed that males possess up to 15 out of 17 of their chromosomes as sex-linked (sex and neo-sex) chromosomes and that they maintain significantly higher levels of heterozygosity than do females. Furthermore, we showed that two obligately asexual lineages of this species-representing the only known all-female termite populations-arose independently via intraspecific hybridization between sexual lineages with differing diploid chromosome numbers. Importantly, these asexual females have markedly higher heterozygosity than their conspecific males and appear to have replaced the sexual lineages in some populations. Our results indicate that asexuality has enabled females to supplant a key role of males.
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Affiliation(s)
- Toshihisa Yashiro
- School of Life and Environmental Sciences, University of Sydney, Sydney NSW 2006, Australia;
- Laboratory of Insect Ecology, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Yi-Kai Tea
- School of Life and Environmental Sciences, University of Sydney, Sydney NSW 2006, Australia
- Ichthyology, Australian Museum Research Institute, Sydney, NSW 2010, Australia
| | - Cara Van Der Wal
- School of Life and Environmental Sciences, University of Sydney, Sydney NSW 2006, Australia
| | - Tomonari Nozaki
- Laboratory of Evolutionary Genomics, National Institute for Basic Biology, Okazaki 444-8585, Japan
| | - Nobuaki Mizumoto
- Evolutionary Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna-son 904-0495, Japan
| | - Simon Hellemans
- Evolutionary Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna-son 904-0495, Japan
| | - Kenji Matsuura
- Laboratory of Insect Ecology, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Nathan Lo
- School of Life and Environmental Sciences, University of Sydney, Sydney NSW 2006, Australia;
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Genetic diversity and population structure of ridge gourd (Luffa acutangula) accessions in a Thailand collection using SNP markers. Sci Rep 2021; 11:15311. [PMID: 34321535 PMCID: PMC8319206 DOI: 10.1038/s41598-021-94802-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 07/16/2021] [Indexed: 11/23/2022] Open
Abstract
This study explored a germplasm collection consisting of 112 Luffa acutangula (ridge gourd) accessions, mainly from Thailand. A total of 2834 SNPs were used to establish population structure and underlying genetic diversity while exploring the fruit characteristics together with genetic information which would help in the selection of parental lines for a breeding program. The study found that the average polymorphism information content value of 0.288 which indicates a moderate genetic diversity for this L. acutangula germplasm. STRUCTURE analysis (ΔK at K = 6) allowed us to group the accessions into six subpopulations that corresponded well with the unrooted phylogenetic tree and principal coordinate analyses. When plotted, the STRUCTURE bars to the area of collection, we observed an admixed genotype from surrounding accessions and a geneflow confirmed by the value of FST = 0.137. AMOVA based on STRUCTURE clustering showed a low 12.83% variation between subpopulations that correspond well with the negative inbreeding coefficient value (FIS = − 0.092) and low total fixation index (FIT = 0.057). There were distinguishing fruit shapes and length characteristics in specific accessions for each subpopulation. The genetic diversity and different fruit shapes in the L. acutangula germplasm could benefit the ridge gourd breeding programs to meet the demands and needs of consumers, farmers, and vegetable exporters such as increasing the yield of fruit by the fruit width but not by the fruit length to solve the problem of fruit breakage during exportation.
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Adu BG, Akromah R, Amoah S, Nyadanu D, Yeboah A, Aboagye LM, Amoah RA, Owusu EG. High-density DArT-based SilicoDArT and SNP markers for genetic diversity and population structure studies in cassava (Manihot esculenta Crantz). PLoS One 2021; 16:e0255290. [PMID: 34314448 PMCID: PMC8315537 DOI: 10.1371/journal.pone.0255290] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 07/14/2021] [Indexed: 11/23/2022] Open
Abstract
Cassava (Manihot esculenta Crantz) is an important industrial and staple crop due to its high starch content, low input requirement, and resilience which makes it an ideal crop for sustainable agricultural systems and marginal lands in the tropics. However, the lack of genomic information on local genetic resources has impeded efficient conservation and improvement of the crop and the exploration of its full agronomic and breeding potential. This work was carried out to obtain information on population structure and extent of genetic variability among some local landraces conserved at the Plant Genetic Resources Research Institute, Ghana and exotic cassava accessions with Diversity Array Technology based SilicoDArT and SNP markers to infer how the relatedness in the genetic materials can be used to enhance germplasm curation and future breeding efforts. A total of 10521 SilicoDArT and 10808 SNP markers were used with varying polymorphic information content (PIC) values. The average PIC was 0.36 and 0.28 for the SilicoDArT and SNPs respectively. Population structure and average linkage hierarchical clustering based on SNPs revealed two distinct subpopulations and a large number of admixtures. Both DArT platforms identified 22 landraces as potential duplicates based on Gower's genetic dissimilarity. The expected heterozygosity which defines the genetic variation within each subpopulation was 0.008 for subpop1 which were mainly landraces and 0.391 for subpop2 indicating the homogeneous and admixture nature of the two subpopulations. Further analysis upon removal of the duplicates increased the expected heterozygosity of subpop1 from 0.008 to 0.357. A mantel test indicated strong interdependence (r = 0.970; P < 0.001) between SilicoDArT and DArTSeq SNP genotypic data suggesting both marker platforms as a robust system for genomic studies in cassava. These findings provide important information for efficient ex-situ conservation of cassava, future heterosis breeding, and marker-assisted selection (MAS) to enhance cassava improvement.
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Affiliation(s)
- Bright Gyamfi Adu
- Council for Scientific and Industrial Research-Plant Genetics Resources Research Institute, Bunso, Ghana
| | - Richard Akromah
- Department of Crop and Soil Sciences, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Stephen Amoah
- Department of Crop and Soil Sciences, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | | | - Alex Yeboah
- Council for Scientific and Industrial Research -Savanna Agricultural Research Institute, Tamale, Ghana
| | - Lawrence Missah Aboagye
- Council for Scientific and Industrial Research-Plant Genetics Resources Research Institute, Bunso, Ghana
| | - Richard Adu Amoah
- Council for Scientific and Industrial Research-Plant Genetics Resources Research Institute, Bunso, Ghana
| | - Eva Gyamfuaa Owusu
- Department of Statistics and Actuarial Sciences, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
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24
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Maity A, Lamichaney A, Joshi DC, Bajwa A, Subramanian N, Walsh M, Bagavathiannan M. Seed Shattering: A Trait of Evolutionary Importance in Plants. FRONTIERS IN PLANT SCIENCE 2021; 12:657773. [PMID: 34220883 PMCID: PMC8248667 DOI: 10.3389/fpls.2021.657773] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 05/21/2021] [Indexed: 05/26/2023]
Abstract
Seed shattering refers to the natural shedding of seeds when they ripe, a phenomenon typically observed in wild and weedy plant species. The timing and extent of this phenomenon varies considerably among plant species. Seed shattering is primarily a genetically controlled trait; however, it is significantly influenced by environmental conditions, management practices and their interactions, especially in agro-ecosystems. This trait is undesirable in domesticated crops where consistent efforts have been made to minimize it through conventional and molecular breeding approaches. However, this evolutionary trait serves as an important fitness and survival mechanism for most weeds that utilize it to ensure efficient dispersal of their seeds, paving the way for persistent soil seedbank development and sustained future populations. Weeds have continuously evolved variations in seed shattering as an adaptation under changing management regimes. High seed retention is common in many cropping weeds where weed maturity coincides with crop harvest, facilitating seed dispersal through harvesting operations, though some weeds have notoriously high seed shattering before crop harvest. However, high seed retention in some of the most problematic agricultural weed species such as annual ryegrass (Lolium rigidum), wild radish (Raphanus raphanistrum), and weedy amaranths (Amaranthus spp.) provides an opportunity to implement innovative weed management approaches such as harvest weed seed control, which aims at capturing and destroying weed seeds retained at crop harvest. The integration of such management options with other practices is important to avoid the rapid evolution of high seed shattering in target weed species. Advances in genetics and molecular biology have shown promise for reducing seed shattering in important crops, which could be exploited for manipulating seed shattering in weed species. Future research should focus on developing a better understanding of various seed shattering mechanisms in plants in relation to changing climatic and management regimes.
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Affiliation(s)
- Aniruddha Maity
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, United States
- Seed Technology Division, ICAR-Indian Grassland and Fodder Research Institute, Jhansi, India
| | - Amrit Lamichaney
- Division of Crop Improvement, ICAR-Indian Institute of Pulses Research, Kanpur, India
| | - Dinesh Chandra Joshi
- Division of Crop Improvement, ICAR-Vivekananda Parvatiya Krishi Anusandhan Sansthan, Almora, India
| | - Ali Bajwa
- Weed Research Unit, New South Wales Department of Primary Industries, Wagga Wagga, NSW, Australia
| | - Nithya Subramanian
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, United States
| | - Michael Walsh
- Sydney Institute of Agriculture, The University of Sydney, Sydney, NSW, Australia
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25
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Quezada-Martinez D, Addo Nyarko CP, Schiessl SV, Mason AS. Using wild relatives and related species to build climate resilience in Brassica crops. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:1711-1728. [PMID: 33730183 PMCID: PMC8205867 DOI: 10.1007/s00122-021-03793-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 02/12/2021] [Indexed: 05/18/2023]
Abstract
Climate change will have major impacts on crop production: not just increasing drought and heat stress, but also increasing insect and disease loads and the chance of extreme weather events and further adverse conditions. Often, wild relatives show increased tolerances to biotic and abiotic stresses, due to reduced stringency of selection for yield and yield-related traits under optimum conditions. One possible strategy to improve resilience in our modern-day crop cultivars is to utilize wild relative germplasm in breeding, and attempt to introgress genetic factors contributing to greater environmental tolerances from these wild relatives into elite crop types. However, this approach can be difficult, as it relies on factors such as ease of hybridization and genetic distance between the source and target, crossover frequencies and distributions in the hybrid, and ability to select for desirable introgressions while minimizing linkage drag. In this review, we outline the possible effects that climate change may have on crop production, introduce the Brassica crop species and their wild relatives, and provide an index of useful traits that are known to be present in each of these species that may be exploitable through interspecific hybridization-based approaches. Subsequently, we outline how introgression breeding works, what factors affect the success of this approach, and how this approach can be optimized so as to increase the chance of recovering the desired introgression lines. Our review provides a working guide to the use of wild relatives and related crop germplasm to improve biotic and abiotic resistances in Brassica crop species.
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Affiliation(s)
- Daniela Quezada-Martinez
- Plant Breeding Department, Justus Liebig University, 35392, Giessen, Germany
- Plant Breeding Department, The University of Bonn, Katzenburgweg 5, 53115, Bonn, Germany
| | - Charles P Addo Nyarko
- Plant Breeding Department, Justus Liebig University, 35392, Giessen, Germany
- Plant Breeding Department, The University of Bonn, Katzenburgweg 5, 53115, Bonn, Germany
| | - Sarah V Schiessl
- Plant Breeding Department, Justus Liebig University, 35392, Giessen, Germany
| | - Annaliese S Mason
- Plant Breeding Department, Justus Liebig University, 35392, Giessen, Germany.
- Plant Breeding Department, The University of Bonn, Katzenburgweg 5, 53115, Bonn, Germany.
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26
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Quezada-Martinez D, Addo Nyarko CP, Schiessl SV, Mason AS. Using wild relatives and related species to build climate resilience in Brassica crops. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:1711-1728. [PMID: 33730183 DOI: 10.1007/s00122-021-03793-3.pdf] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 02/12/2021] [Indexed: 05/24/2023]
Abstract
Climate change will have major impacts on crop production: not just increasing drought and heat stress, but also increasing insect and disease loads and the chance of extreme weather events and further adverse conditions. Often, wild relatives show increased tolerances to biotic and abiotic stresses, due to reduced stringency of selection for yield and yield-related traits under optimum conditions. One possible strategy to improve resilience in our modern-day crop cultivars is to utilize wild relative germplasm in breeding, and attempt to introgress genetic factors contributing to greater environmental tolerances from these wild relatives into elite crop types. However, this approach can be difficult, as it relies on factors such as ease of hybridization and genetic distance between the source and target, crossover frequencies and distributions in the hybrid, and ability to select for desirable introgressions while minimizing linkage drag. In this review, we outline the possible effects that climate change may have on crop production, introduce the Brassica crop species and their wild relatives, and provide an index of useful traits that are known to be present in each of these species that may be exploitable through interspecific hybridization-based approaches. Subsequently, we outline how introgression breeding works, what factors affect the success of this approach, and how this approach can be optimized so as to increase the chance of recovering the desired introgression lines. Our review provides a working guide to the use of wild relatives and related crop germplasm to improve biotic and abiotic resistances in Brassica crop species.
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Affiliation(s)
- Daniela Quezada-Martinez
- Plant Breeding Department, Justus Liebig University, 35392, Giessen, Germany
- Plant Breeding Department, The University of Bonn, Katzenburgweg 5, 53115, Bonn, Germany
| | - Charles P Addo Nyarko
- Plant Breeding Department, Justus Liebig University, 35392, Giessen, Germany
- Plant Breeding Department, The University of Bonn, Katzenburgweg 5, 53115, Bonn, Germany
| | - Sarah V Schiessl
- Plant Breeding Department, Justus Liebig University, 35392, Giessen, Germany
| | - Annaliese S Mason
- Plant Breeding Department, Justus Liebig University, 35392, Giessen, Germany.
- Plant Breeding Department, The University of Bonn, Katzenburgweg 5, 53115, Bonn, Germany.
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Raman H, Raman R, Qiu Y, Zhang Y, Batley J, Liu S. The Rlm13 Gene, a New Player of Brassica napus- Leptosphaeria maculans Interaction Maps on Chromosome C03 in Canola. FRONTIERS IN PLANT SCIENCE 2021; 12:654604. [PMID: 34054900 PMCID: PMC8150007 DOI: 10.3389/fpls.2021.654604] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Accepted: 03/25/2021] [Indexed: 05/24/2023]
Abstract
Canola exhibits an extensive genetic variation for resistance to blackleg disease, caused by the fungal pathogen Leptosphaeria maculans. Despite the identification of several Avr effectors and R (race-specific) genes, specific interactions between Avr-R genes are not yet fully understood in the Brassica napus-L. maculans pathosystem. In this study, we investigated the genetic basis of resistance in an F2 : 3 population derived from Australian canola varieties CB-Telfer (Rlm4)/ATR-Cobbler (Rlm4) using a single-spore isolate of L. maculans, PHW1223. A genetic linkage map of the CB-Telfer/ATR-Cobbler population was constructed using 7,932 genotyping-by-sequencing-based DArTseq markers and subsequently utilized for linkage and haplotype analyses. Genetic linkage between DArTseq markers and resistance to PHW1223 isolate was also validated using the B. napus 60K Illumina Infinium array. Our results revealed that a major locus for resistance, designated as Rlm13, maps on chromosome C03. To date, no R gene for resistance to blackleg has been reported on the C subgenome in B. napus. Twenty-four candidate R genes were predicted to reside within the quantitative trait locus (QTL) region. We further resequenced both the parental lines of the mapping population (CB-Telfer and ATR-Cobbler, > 80 × coverage) and identified several structural sequence variants in the form of single-nucleotide polymorphisms (SNPs), insertions/deletions (InDels), and presence/absence variations (PAVs) near Rlm13. Comparative mapping revealed that Rlm13 is located within the homoeologous A03/C03 region in ancestral karyotype block "R" of Brassicaceae. Our results provide a "target" for further understanding the Avr-Rlm13 gene interaction as well as a valuable tool for increasing resistance to blackleg in canola germplasm.
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Affiliation(s)
- Harsh Raman
- NSW Department of Primary Industries, Wagga Wagga Agricultural Institute, Wagga Wagga, NSW, Australia
| | - Rosy Raman
- NSW Department of Primary Industries, Wagga Wagga Agricultural Institute, Wagga Wagga, NSW, Australia
| | - Yu Qiu
- NSW Department of Primary Industries, Wagga Wagga Agricultural Institute, Wagga Wagga, NSW, Australia
| | - Yuanyuan Zhang
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Jacqueline Batley
- School of Biological Sciences, University of Western Australia, Crawley, WA, Australia
| | - Shengyi Liu
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
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28
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Łangowski Ł, Goñi O, Marques FS, Hamawaki OT, da Silva CO, Nogueira APO, Teixeira MAJ, Glasenapp JS, Pereira M, O’Connell S. Ascophyllum nodosum Extract (Sealicit TM) Boosts Soybean Yield Through Reduction of Pod Shattering-Related Seed Loss and Enhanced Seed Production. FRONTIERS IN PLANT SCIENCE 2021; 12:631768. [PMID: 33719306 PMCID: PMC7943832 DOI: 10.3389/fpls.2021.631768] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 01/25/2021] [Indexed: 05/27/2023]
Abstract
Soybean is one of the most valuable commercial crops because of its high protein, carbohydrate, and oil content. The land area cultivated with soybean in subtropical regions, such as Brazil, is continuously expanding, in some instances at the expense of carbon storing natural habitats. Strategies to decrease yield/seed losses and increase production efficiency are urgently required to meet global demand for soybean in a sustainable manner. Here, we evaluated the effectiveness of an Ascophyllum nodosum extract (ANE), SealicitTM, in increasing yields of different soybean varieties, in two geographical regions (Canada and Brazil). In addition, we investigated the potential of SealicitTM to reduce pod shattering at the trials in Brazil. Three different concentrations of SealicitTM were applied to pod shatter-susceptible (SS) UFUS 6901 and shatter-resistant (SR) UFUS 7415 varieties to assess their impact on pod firmness. SS variety demonstrated a significant decrease in pod shattering, which coincided with deregulation of GmPDH1.1 and GmSHAT1-5 expression, genes that determine pod dehiscence, and higher seed weight per pod. SealicitTM application to the SR variety did not significantly alter its inherent pod shatter resistance, but provided higher increases in seed yield at harvest. This yield increase maybe associated with to other yield components stimulated by the biostimulant. This work demonstrates that SealicitTM, which has previously been shown to improve pod firmness in Arabidopsis and selected commercial oilseed rape varieties through IND gene down-regulation, also has the potential to improve pod resistance and seed productivity in soybean, a member of the legume family sharing a similar strategy for seed dispersal.
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Affiliation(s)
| | - Oscar Goñi
- Plant Biostimulant Group, Shannon Applied Biotechnology Centre, Munster Technological University Kerry, Tralee, Ireland
| | - Fabio Serafim Marques
- Instituto de Ciências Agrárias, Universidade Federal de Uberlândia/UFU, Uberlândia, Brazil
| | | | | | | | | | | | - Marcio Pereira
- Fundação Educacional de Ituverava FAFRAM, Faculdade Agronomia, Ituverava, Brazil
| | - Shane O’Connell
- Plant Biostimulant Group, Shannon Applied Biotechnology Centre, Munster Technological University Kerry, Tralee, Ireland
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Badu-Apraku B, Garcia-Oliveira AL, Petroli CD, Hearne S, Adewale SA, Gedil M. Genetic diversity and population structure of early and extra-early maturing maize germplasm adapted to sub-Saharan Africa. BMC PLANT BIOLOGY 2021; 21:96. [PMID: 33596835 PMCID: PMC7888073 DOI: 10.1186/s12870-021-02829-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 01/07/2021] [Indexed: 05/25/2023]
Abstract
BACKGROUND Assessment and effective utilization of genetic diversity in breeding programs is crucial for sustainable genetic improvement and rapid adaptation to changing breeding objectives. During the past two decades, the commercialization of the early and extra-early maturing cultivars has contributed to rapid expansion of maize into different agro-ecologies of sub-Saharan Africa (SSA) where maize has become an important component of the agricultural economy and played a vital role in food and nutritional security. The present study aimed at understanding the population structure and genetic variability among 439 early and extra-early maize inbred lines developed from three narrow-based and twenty-seven broad-based populations by the International Iinstitute of Tropical Agriculture Maize Improvement Program (IITA-MIP). These inbreds were genotyped using 9642 DArTseq-based single nucleotide polymorphism (SNP) markers distributed uniformly throughout the maize genome. RESULTS About 40.8% SNP markers were found highly informative and exhibited polymorphic information content (PIC) greater than 0.25. The minor allele frequency and PIC ranged from 0.015 to 0.500 and 0.029 to 0.375, respectively. The STRUCTURE, neighbour-joining phylogenetic tree and principal coordinate analysis (PCoA) grouped the inbred lines into four major classes generally consistent with the selection history, ancestry and kernel colour of the inbreds but indicated a complex pattern of the genetic structure. The pattern of grouping of the lines based on the STRUCTURE analysis was in concordance with the results of the PCoA and suggested greater number of sub-populations (K = 10). Generally, the classification of the inbred lines into heterotic groups based on SNP markers was reasonably reliable and in agreement with defined heterotic groups of previously identified testers based on combining ability studies. CONCLUSIONS Complete understanding of potential heterotic groups would be difficult to portray by depending solely on molecular markers. Therefore, planned crosses involving representative testers from opposing heterotic groups would be required to refine the existing heterotic groups. It is anticipated that the present set of inbreds could contribute new beneficial alleles for population improvement, development of hybrids and lines with potential to strengthen future breeding programs. Results of this study would help breeders in formulating breeding strategies for genetic enhancement and sustainable maize production in SSA.
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Affiliation(s)
- Baffour Badu-Apraku
- International Institute of Tropical Agriculture (IITA), PMB 5320, Oyo Rd, Ibadan, 200001 Nigeria
| | - Ana Luísa Garcia-Oliveira
- International Institute of Tropical Agriculture (IITA), PMB 5320, Oyo Rd, Ibadan, 200001 Nigeria
- International Maize and Wheat Improvement Center (CIMMYT), Carretera México-Veracruz Km. 45 El Batán, 56237 Texcoco, Mexico
| | - César Daniel Petroli
- International Maize and Wheat Improvement Center (CIMMYT), Carretera México-Veracruz Km. 45 El Batán, 56237 Texcoco, Mexico
| | - Sarah Hearne
- International Maize and Wheat Improvement Center (CIMMYT), Carretera México-Veracruz Km. 45 El Batán, 56237 Texcoco, Mexico
| | - Samuel Adeyemi Adewale
- International Institute of Tropical Agriculture (IITA), PMB 5320, Oyo Rd, Ibadan, 200001 Nigeria
| | - Melaku Gedil
- International Institute of Tropical Agriculture (IITA), PMB 5320, Oyo Rd, Ibadan, 200001 Nigeria
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In-Depth Genetic Diversity and Population Structure of Endangered Peruvian Amazon Rosewood Germplasm Using Genotyping by Sequencing (GBS) Technology. FORESTS 2021. [DOI: 10.3390/f12020197] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Research studies on conservative genetics of endangered plants are very important to establish the management plans for the conservation of biodiversity. Rosewood is an evergreen tree of the Amazon region and its essential oil has great acceptance in the medical and cosmetic industry. The present study aimed to explore the genetic diversity and population structure of 90 rosewood accessions collected from eight localities of Peruvian Amazon territory through DArTseq markers. A total of 7485 informative markers resulted from genotyping by sequencing (GBS) analysis were used for the molecular characterization of rosewood germplasm. Mean values of various calculated diversity parameters like observed number of alleles (1.962), the effective number of alleles (1.669), unbiased expected heterozygosity (0.411), and percent polymorphism (93.51%) over the entire germplasm showed the existence of a good level of genetic variations. Our results showed that the Mairiricay population was more diverse compared to the rest of the populations. Tamshiyacu-2 and Mairiricay-15 accessions were found genetically distinct accessions. The analysis of molecular variance (AMOVA) reflected maximum variations (75%) are due to differences within populations. The implemented clustering algorithms, i.e., STRUCTURE, neighbor-joining analysis and principal coordinate analysis (PCoA) separated the studied germplasm on the basis of their geographical locations. Diversity indices for STRUCTURE-based populations showed that subpopulation A is more diverse population than the rest of the populations, for such reason, individuals belonging to this subpopulation should be used for reintroduction or reinforcement plans of rosewood conservation. We envisage that molecular characterization of Peruvian rosewood germplasm with DArTseq markers will provide a platform for the conservation, management and restoration of endangered rosewood in upcoming years.
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31
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Couch AJ, Dyer F, Lintermans M. Multi-year pair-bonding in Murray cod ( Maccullochella peelii). PeerJ 2020; 8:e10460. [PMID: 33354425 PMCID: PMC7733648 DOI: 10.7717/peerj.10460] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 11/10/2020] [Indexed: 01/20/2023] Open
Abstract
Mating strategies in fishes are known to include polygyny, polyandry and monogamy and provide valuable insights regarding powerful evolutionary forces such as sexual selection. Monogamy is a complex of mating systems that has been relatively neglected. Previous work on mating strategies in fishes has often been based on observation and focused on marine species rather than freshwater fishes. SNPs are increasingly being used as a molecular ecology tool in non-model organisms, and methods of probabilistic genetic analysis of such datasets are becoming available for use in the absence of parental genotypes. This approach can be used to infer mating strategies. The long-term pair bonding seen in mammals, reptiles and birds has not been recorded in freshwater fishes-in every other respect an extremely diverse group. This study shows that multi-year pair bonding occurs in an Australian Percichthyid fish that exhibits paternal care of eggs and larvae. Using SNPs, full sibling pairs of larvae were found over multiple years in a three-year study. Stable isotope signatures of the larvae support the genetic inference that full sibling pairs shared a common mother, the ultimate source of that isotopic signature during oogenesis. Spatial and temporal clustering also suggests that the full sibling larvae are unlikely to be false positive identifications of the probabilistic identification of siblings. For the first time, we show multi-year pair bonding in a wild freshwater fish. This will have important conservation and management implications for the species. This approach could provide insights into many behavioural, ecological and evolutionary questions, particularly if this is not a unique case. Our findings are likely to initiate interest in seeking more examples of monogamy and alternative mating strategies in freshwater fishes, particularly if others improve methods of analysis of SNP data for identification of siblings in the absence of parental genotypes.
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Affiliation(s)
- Alan J Couch
- Centre for Applied Water Science, University of Canberra, Canberra, ACT, Australia
| | - Fiona Dyer
- Centre for Applied Water Science, University of Canberra, Canberra, ACT, Australia
| | - Mark Lintermans
- Centre for Applied Water Science, University of Canberra, Canberra, ACT, Australia
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32
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Gemenet DC, Lindqvist-Kreuze H, De Boeck B, da Silva Pereira G, Mollinari M, Zeng ZB, Craig Yencho G, Campos H. Sequencing depth and genotype quality: accuracy and breeding operation considerations for genomic selection applications in autopolyploid crops. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:3345-3363. [PMID: 32876753 PMCID: PMC7567692 DOI: 10.1007/s00122-020-03673-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Accepted: 08/21/2020] [Indexed: 05/06/2023]
Abstract
KEY MESSAGE Polypoid crop breeders can balance resources between density and sequencing depth, dosage information and fewer highly informative SNPs recommended, non-additive models and QTL advantages on prediction dependent on trait architecture. The autopolyploid nature of potato and sweetpotato ensures a wide range of meiotic configurations and linkage phases leading to complex gene-action and pose problems in genotype data quality and genomic selection analyses. We used a 315-progeny biparental F1 population of hexaploid sweetpotato and a diversity panel of 380 tetraploid potato, genotyped using different platforms to answer the following questions: (i) do polyploid crop breeders need to invest more for additional sequencing depth? (ii) how many markers are required to make selection decisions? (iii) does considering non-additive genetic effects improve predictive ability (PA)? (iv) does considering dosage or quantitative trait loci (QTL) offer significant improvement to PA? Our results show that only a small number of highly informative single nucleotide polymorphisms (SNPs; ≤ 1000) are adequate for prediction in the type of populations we analyzed. We also show that considering dosage information and models considering only additive effects had the best PA for most traits, while the comparative advantage of considering non-additive genetic effects and including known QTL in the predictive model depended on trait architecture. We conclude that genomic selection can help accelerate the rate of genetic gains in potato and sweetpotato. However, application of genomic selection should be considered as part of optimizing the entire breeding program. Additionally, since the predictions in the current study are based on single populations, further studies on the effects of haplotype structure and inheritance on PA should be studied in actual multi-generation breeding populations.
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Affiliation(s)
- Dorcus C Gemenet
- International Potato Center, ILRI Campus, P.O. Box 25171-00603, Nairobi, Kenya.
- CGIAR Excellence in Breeding Platform, International Maize and Wheat Improvement Center (CIMMYT), ICRAF Campus, 1041-00621, Nairobi, Kenya.
| | | | - Bert De Boeck
- International Potato Center, Av. La Molina 1895, Lima, Peru
| | | | | | - Zhao-Bang Zeng
- North Carolina State University, Raleigh, NC, 27695, USA
| | - G Craig Yencho
- North Carolina State University, Raleigh, NC, 27695, USA
| | - Hugo Campos
- International Potato Center, Av. La Molina 1895, Lima, Peru
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33
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Nayfa MG, Jones DB, Benzie JAH, Jerry DR, Zenger KR. Comparing Genomic Signatures of Selection Between the Abbassa Strain and Eight Wild Populations of Nile Tilapia ( Oreochromis niloticus) in Egypt. Front Genet 2020; 11:567969. [PMID: 33193660 PMCID: PMC7593532 DOI: 10.3389/fgene.2020.567969] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 08/31/2020] [Indexed: 11/16/2022] Open
Abstract
Domestication to captive rearing conditions, along with targeted selective breeding have genetic consequences that vary from those in wild environments. Nile tilapia (Oreochromis niloticus) is one of the most translocated and farmed aquaculture species globally, farmed throughout Asia, North and South America, and its African native range. In Egypt, a breeding program established the Abbassa Strain of Nile tilapia (AS) in 2002 based on local broodstock sourced from the Nile River. The AS has been intensively selected for growth and has gone through genetic bottlenecks which have likely shifted levels and composition of genetic diversity within the strain. Consequently, there are questions on the possible genetic impact AS escapees may have on endemic populations of Nile tilapia. However, to date there have been no genetic studies comparing genetic changes in the domesticated AS to local wild populations. This study used 9,827 genome-wide SNPs to investigate population genetic structure and signatures of selection in the AS (generations 9–11) and eight wild Nile tilapia populations from Egypt. SNP analyses identified two major genetic clusters (captive and wild populations), with wild populations showing evidence of isolation-by-distance among the Nile Delta and upstream riverine populations. Between genetic clusters, approximately 6.9% of SNPs were identified as outliers with outliers identified on all 22 O. niloticus chromosomes. A lack of localized outlier clustering on the genome suggests that no genes of major effect were presently detected. The AS has retained high levels of genetic diversity (Ho_All = 0.21 ± 0.01; He_All = 0.23 ± 0.01) when compared to wild populations (Ho_All = 0.18 ± 0.01; He_All = 0.17 ± 0.01) after 11 years of domestication and selective breeding. Additionally, 565 SNPs were unique within the AS line. While these private SNPs may be due to domestication signals or founder effects, it is suspected that introgression with blue tilapia (Oreochromis aureus) has occurred. This study highlights the importance of understanding the effects of domestication in addition to wild population structure to inform future management and dissemination decisions. Furthermore, by conducting a baseline genetic study of wild populations prior to the dissemination of a domestic line, the effects of aquaculture on these populations can be monitored over time.
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Affiliation(s)
- Maria G Nayfa
- Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, QLD, Australia.,Centre for Tropical Bioinformatics and Molecular Biology, College of Science and Engineering, James Cook University, Townsville, QLD, Australia
| | - David B Jones
- Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, QLD, Australia.,Centre for Tropical Bioinformatics and Molecular Biology, College of Science and Engineering, James Cook University, Townsville, QLD, Australia
| | - John A H Benzie
- WorldFish, Penang, Malaysia.,School of Biological, Earth and Environmental Sciences, University College Cork, Cork, Ireland
| | - Dean R Jerry
- Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, QLD, Australia.,Centre for Tropical Bioinformatics and Molecular Biology, College of Science and Engineering, James Cook University, Townsville, QLD, Australia.,Tropical Futures Institute, James Cook University, Singapore, Singapore
| | - Kyall R Zenger
- Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, QLD, Australia.,Centre for Tropical Bioinformatics and Molecular Biology, College of Science and Engineering, James Cook University, Townsville, QLD, Australia
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Liu J, Zhou R, Wang W, Wang H, Qiu Y, Raman R, Mei D, Raman H, Hu Q. A copia-like retrotransposon insertion in the upstream region of the SHATTERPROOF1 gene, BnSHP1.A9, is associated with quantitative variation in pod shattering resistance in oilseed rape. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:5402-5413. [PMID: 32525990 PMCID: PMC7501816 DOI: 10.1093/jxb/eraa281] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 06/10/2020] [Indexed: 05/03/2023]
Abstract
Seed loss resulting from pod shattering is a major constraint in production of oilseed rape (Brassica napus L.). However, the molecular mechanisms underlying pod shatter resistance are not well understood. Here, we show that the pod shatter resistance at quantitative trait locus qSRI.A9.1 is controlled by one of the B. napus SHATTERPROOF1 homologs, BnSHP1.A9, in a doubled haploid population generated from parents designated R1 and R2 as well as in a diverse panel of oilseed rape. The R1 maternal parental line of the doubled haploid population carried the allele for shattering at qSRI.A9.1, while the R2 parental line carried the allele for shattering resistance. Quantitative RT-PCR showed that BnSHP1.A9 was expressed specifically in flower buds, flowers, and developing siliques in R1, while it was not expressed in any tissue of R2. Transgenic plants constitutively expressing either of the BnSHP1.A9 alleles from the R1 and R2 parental lines showed that both alleles are responsible for pod shattering, via a mechanism that promotes lignification of the enb layer. These findings indicated that the allelic differences in the BnSHP1.A9 gene per se are not the causal factor for quantitative variation in shattering resistance at qSRI.A9.1. Instead, a highly methylated copia-like long terminal repeat retrotransposon insertion (4803 bp) in the promotor region of the R2 allele of BnSHP1.A9 repressed the expression of BnSHP1.A9, and thus contributed to pod shatter resistance. Finally, we showed a copia-like retrotransposon-based marker, BnSHP1.A9R2, can be used for marker-assisted breeding targeting the pod shatter resistance trait in oilseed rape.
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Affiliation(s)
- Jia Liu
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan Hubei, P.R. China
| | - Rijin Zhou
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan Hubei, P.R. China
| | - Wenxiang Wang
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan Hubei, P.R. China
| | - Hui Wang
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan Hubei, P.R. China
| | - Yu Qiu
- NSW Department of Primary Industries, Wagga Wagga Agricultural Institute, PMB, Wagga Wagga, NSW, Australia
| | - Rosy Raman
- NSW Department of Primary Industries, Wagga Wagga Agricultural Institute, PMB, Wagga Wagga, NSW, Australia
| | - Desheng Mei
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan Hubei, P.R. China
| | - Harsh Raman
- NSW Department of Primary Industries, Wagga Wagga Agricultural Institute, PMB, Wagga Wagga, NSW, Australia
| | - Qiong Hu
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan Hubei, P.R. China
- Correspondence:
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35
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Fikere M, Barbulescu DM, Malmberg MM, Spangenberg GC, Cogan NOI, Daetwyler HD. Meta-analysis of GWAS in canola blackleg (Leptosphaeria maculans) disease traits demonstrates increased power from imputed whole-genome sequence. Sci Rep 2020; 10:14300. [PMID: 32868838 PMCID: PMC7459325 DOI: 10.1038/s41598-020-71274-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Accepted: 08/13/2020] [Indexed: 12/21/2022] Open
Abstract
Blackleg disease causes yield losses in canola (Brassica napus L.). To identify resistance genes and genomic regions, genome-wide association studies (GWAS) of 585 diverse winter and spring canola accessions were performed using imputed whole-genome sequence (WGS) and transcriptome genotype-by-sequencing (GBSt). Blackleg disease phenotypes were collected across three years in six trials. GWAS were performed in several ways and their respective power was judged by the number of significant single nucleotide polymorphisms (SNP), the false discovery rate (FDR), and the percentage of SNP that validated in additional field trials in two subsequent years. WGS GWAS with 1,234,708 million SNP detected a larger number of significant SNP, achieved a lower FDR and a higher validation rate than GBSt with 64,072 SNP. A meta-analysis combining survival and average internal infection resulted in lower FDR but also lower validation rates. The meta-analysis GWAS identified 79 genomic regions (674 SNP) conferring potential resistance to L. maculans. While several GWAS signals localised in regions of known Rlm genes, fifty-three new potential resistance regions were detected. Seventeen regions had underlying genes with putative functions related to disease defence or stress response in Arabidopsis thaliana. This study provides insight into the genetic architecture and potential molecular mechanisms underlying canola L. maculans resistance.
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Affiliation(s)
- M Fikere
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, 3086, Australia.,Centre for AgriBioscience, Agriculture Victoria, AgriBio, Bundoora, VIC, 3083, Australia.,Queensland Alliance for Agriculture and Food Innovation (QAAFI), The University of Queensland, Brisbane, QLD, 4072, Australia
| | - D M Barbulescu
- Agriculture Victoria, Grains Innovation Park, Horsham, VIC, 3401, Australia
| | - M M Malmberg
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, 3086, Australia.,Centre for AgriBioscience, Agriculture Victoria, AgriBio, Bundoora, VIC, 3083, Australia
| | - G C Spangenberg
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, 3086, Australia.,Centre for AgriBioscience, Agriculture Victoria, AgriBio, Bundoora, VIC, 3083, Australia
| | - N O I Cogan
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, 3086, Australia.,Centre for AgriBioscience, Agriculture Victoria, AgriBio, Bundoora, VIC, 3083, Australia
| | - H D Daetwyler
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, 3086, Australia. .,Centre for AgriBioscience, Agriculture Victoria, AgriBio, Bundoora, VIC, 3083, Australia.
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36
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Baiakhmetov E, Nowak A, Gudkova PD, Nobis M. Morphological and genome-wide evidence for natural hybridisation within the genus Stipa (Poaceae). Sci Rep 2020; 10:13803. [PMID: 32796878 PMCID: PMC7427808 DOI: 10.1038/s41598-020-70582-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 07/31/2020] [Indexed: 11/17/2022] Open
Abstract
Hybridisation in the wild between closely related species is a common mechanism of speciation in the plant kingdom and, in particular, in the grass family. Here we explore the potential for natural hybridisation in Stipa (one of the largest genera in Poaceae) between genetically distant species at their distribution edges in Mountains of Central Asia using integrative taxonomy. Our research highlights the applicability of classical morphological and genome reduction approaches in studies on wild plant species. The obtained results revealed a new nothospecies, Stipa × lazkovii, which exhibits intermediate characters to S. krylovii and S. bungeana. A high-density DArTseq assay disclosed that S. × lazkovii is an F1 hybrid, and established that the plastid and mitochondrial DNA was inherited from S. bungeana. In addition, molecular markers detected a hybridisation event between morphologically and genetically distant species S. bungeana and probably S. glareosa. Moreover, our findings demonstrated an uncertainty on the taxonomic status of S. bungeana that currently belongs to the section Leiostipa, but it is genetically closer to S. breviflora from the section Barbatae. Finally, we noticed a discrepancy between the current molecular data with the previous findings on S. capillata and S. sareptana.
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Affiliation(s)
- Evgenii Baiakhmetov
- Institute of Botany, Faculty of Biology, Jagiellonian University, Gronostajowa 3, 30-387, Kraków, Poland. .,Research Laboratory 'Herbarium', National Research Tomsk State University, Lenin 36 Ave, 634050, Tomsk, Russia.
| | - Arkadiusz Nowak
- Botanical Garden-Centre for Biological Diversity Conservation, Polish Academy of Sciences, Prawdziwka 2, 02-973, Warszawa, Poland.,Institute of Biology, Opole University, Oleska 22, 45-052, Opole, Poland
| | - Polina D Gudkova
- Research Laboratory 'Herbarium', National Research Tomsk State University, Lenin 36 Ave, 634050, Tomsk, Russia.,Department of Biology, Altai State University, Lenin 61 Ave, 656049, Barnaul, Russia
| | - Marcin Nobis
- Institute of Botany, Faculty of Biology, Jagiellonian University, Gronostajowa 3, 30-387, Kraków, Poland.
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Erdogmus S, Ates D, Nemli S, Yagmur B, Asciogul TK, Ozkuru E, Karaca N, Yilmaz H, Esiyok D, Tanyolac MB. Genome-wide association studies of Ca and Mn in the seeds of the common bean (Phaseolus vulgaris L.). Genomics 2020; 112:4536-4546. [PMID: 32763354 DOI: 10.1016/j.ygeno.2020.03.030] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 03/09/2020] [Accepted: 03/14/2020] [Indexed: 12/16/2022]
Abstract
SNP markers linked to genes controlling Ca and Mn uptake were identified in the common bean seeds using DArT-based association mapping (AM). The Ca concentration in the seeds varied between 475 and 3,100 mg kg-1 with an average of 1,280.9 mg kg-1 and the Mn concentration ranged from 4.87 to 27.54 mg kg-1 with a mean of 11.76 mg kg-1. A total of 19,204 SNP markers were distributed across 11 chromosomes that correspond to the haploid genome number of the common bean. The highest value of ΔK was determined as K = 2, and 173 common bean genotypes were split into two main subclusters as POP1 (Mesoamerican) and POP2 (Andean). The results of the UPGMA dendrogram and PCA confirmed those of STRUCTURE analysis. MLM based on the Q + K model identified a large number of markers-trait associations. Of the 19,204 SNPs, five (on Pv2, 3, 8, 10 and 11) and four (on Pv2, 3, 8 and 11) SNPs were detected to be significantly related to the Ca content of the beans grown in Bornova and Menemen, respectively in 2015. In 2016, six SNPs (on Pv1-4, 8 and 10) were identified to be significantly associated with the Ca content of the seeds obtained from Bornova and six SNPs (on Pv1-4, 8 and 10) from Menemen. Eight (on Pv3, 5 and 11) and four (on Pv2, 5 and 11) SNPs had a significant association with Mn content in Bornova in 2015 and 2016, respectively. In Menemen, eight (on Pv3, 5, 8 and 11) and 11 (on Pv1, 2, 5, 10 and 11) SNPs had a significant correlation with Mn content in 2015 and 2016, respectively.
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Affiliation(s)
- Semih Erdogmus
- Ege University, Department of Bioengineering, Bornova-Izmir 35100, Turkey
| | - Duygu Ates
- Ege University, Department of Bioengineering, Bornova-Izmir 35100, Turkey
| | - Seda Nemli
- Ege University, Faculty of Fisheries, Bornova-Izmir 35100, Turkey
| | - Bulent Yagmur
- Ege University, Department of Soil Science and Plant Nutrition, Bornova-Izmir 35100, Turkey
| | | | - Esin Ozkuru
- Ege University, Department of Bioengineering, Bornova-Izmir 35100, Turkey
| | - Nur Karaca
- Ege University, Department of Bioengineering, Bornova-Izmir 35100, Turkey
| | - Hasan Yilmaz
- Ege University, Department of Bioengineering, Bornova-Izmir 35100, Turkey
| | - Dursun Esiyok
- Ege University, Department of Horticulture, Bornova-Izmir, 35040, Turkey
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Spagopoulou F, Vega-Trejo R, Head ML, Jennions MD. Shifts in Reproductive Investment in Response to Competitors Lower Male Reproductive Success. Am Nat 2020; 196:355-368. [PMID: 32813996 DOI: 10.1086/709821] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
AbstractIn many species, males exhibit phenotypic plasticity in sexually selected traits when exposed to social cues about the intensity of sexual competition. To date, however, few studies have tested how this plasticity affects male reproductive success. We initially tested whether male mosquitofish, Gambusia holbrooki (Poeciliidae), change their investment in traits under pre- and postcopulatory sexual selection depending on the social environment. For a full spermatogenesis cycle, focal males were exposed to visual and chemical cues of rivals that were either present (competitive treatment) or absent (control). Males from the competitive treatment had significantly slower-swimming sperm but did not differ in sperm count from control males. When two males competed for a female, competitive treatment males also made significantly fewer copulation attempts and courtship displays than control males. Further, paternity analysis of 708 offspring from 148 potential sires, testing whether these changes in reproductive traits affected male reproductive success, showed that males previously exposed to cues about the presence of rivals sired significantly fewer offspring when competing with a control male. We discuss several possible explanations for these unusual findings.
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Schultz AJ, Cristescu RH, Hanger J, Loader J, de Villiers D, Frère CH. Inbreeding and disease avoidance in a free-ranging koala population. Mol Ecol 2020; 29:2416-2430. [PMID: 32470998 DOI: 10.1111/mec.15488] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Accepted: 05/11/2020] [Indexed: 11/30/2022]
Abstract
Habitat destruction and fragmentation are increasing globally, forcing surviving species into small, isolated populations. Isolated populations typically experience heightened inbreeding risk and associated inbreeding depression and population decline; although individuals in these populations may mitigate these risks through inbreeding avoidance strategies. For koalas, as dietary specialists already under threat in the northern parts of their range, increased habitat fragmentation and associated inbreeding costs are of great conservation concern. Koalas are known to display passive inbreeding avoidance through sex-biased dispersal, although population isolation will reduce dispersal pathways. We tested whether free-ranging koalas display active inbreeding avoidance behaviours. We used VHF tracking data, parentage reconstruction, and veterinary examination results to test whether free-ranging female koalas avoid mating with (a) more closely related males; and (b) males infected with sexually transmitted Chlamydia pecorum. We found no evidence that female koalas avoid mating with relatively more related available mates. In fact, as the relatedness of potential mates increases, so did inbreeding events. We also found no evidence that female koalas can avoid mating with males infected with C. pecorum. The absence of active inbreeding avoidance mechanisms in koalas is concerning from a conservation perspective, as small, isolated populations may be at even higher risk of inbreeding depression than expected. At risk koala populations may require urgent conservation interventions to augment gene flow and reduce inbreeding risks. Similarly, if koalas are not avoiding mating with individuals with chlamydial disease, populations may be at higher risk from disease than anticipated, further impacting population viability.
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Affiliation(s)
- Anthony J Schultz
- Global Change Ecology Research Group, University of the Sunshine Coast, Sippy Downs, QLD, Australia
| | - Romane H Cristescu
- Global Change Ecology Research Group, University of the Sunshine Coast, Sippy Downs, QLD, Australia
| | - Jon Hanger
- Endeavour Veterinary Ecology Pty Ltd, Toorbul, QLD, Australia
| | - Jo Loader
- Endeavour Veterinary Ecology Pty Ltd, Toorbul, QLD, Australia
| | | | - Celine H Frère
- Global Change Ecology Research Group, University of the Sunshine Coast, Sippy Downs, QLD, Australia
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Curtolo M, Granato LM, Soratto TAT, Curtolo M, Gazaffi R, Takita MA, Cristofani-Yaly M, Machado MA. Expression Quantitative Trait Loci (eQTL) mapping for callose synthases in intergeneric hybrids of Citrus challenged with the bacteria Candidatus Liberibacter asiaticus. Genet Mol Biol 2020; 43:e20190133. [PMID: 32568357 PMCID: PMC7295156 DOI: 10.1590/1678-4685-gmb-2019-0133] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Accepted: 01/07/2020] [Indexed: 11/21/2022] Open
Abstract
Citrus plants have been extremely affected by Huanglongbing (HLB) worldwide, causing
economic losses. HLB disease causes disorders in citrus plants, leading to callose
deposition in the phloem vessel sieve plates. Callose is synthesized by callose
synthases, which are encoded by 12 genes (calS1–
calS12)in Arabidopsis thaliana. We evaluated the
expression of eight callose synthase genes from Citrus in hybrids between
Citrus sunki and Poncirus trifoliata infected
with HLB. The objective of this work was to identify possible tolerance loci
combining the expression quantitative trait loci (eQTL) of different callose
synthases and genetic Single-Nucleotide Polymorphism (SNP) maps of C.
sunki and P. trifoliata. The expression data from all
CscalS ranged widely among the hybrids. Furthermore, the data
allowed the detection of 18 eQTL in the C. sunki map and 34 eQTL in
the P. trifoliata map. In both maps, some eQTL for different
CscalS were overlapped; thus, a single region could be associated
with the regulation of more than one CscalS. The regions identified
in this work can be interesting targets for future studies of Citrus
breeding programs to manipulate callose synthesis during HLB infection.
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Affiliation(s)
- Maiara Curtolo
- Instituto Agronômico de Campinas, Centro APTA Citros Sylvio Moreira, Cordeirópolis, SP, Brazil.,Universidade Estadual de Campinas, Programa de Pós-Graduação em Genética e Biologia Molecular, Campinas, SP, Brazil
| | - Laís Moreira Granato
- Instituto Agronômico de Campinas, Centro APTA Citros Sylvio Moreira, Cordeirópolis, SP, Brazil
| | | | - Maisa Curtolo
- Universidade de São Paulo, Escola Superior de Agricultura Luiz de Queiroz, Programa de Pós-Graduação em Genética e Melhoramento de Plantas, Piracicaba, SP, Brazil
| | - Rodrigo Gazaffi
- Universidade Federal de São Carlos, Centro de Ciências Agrárias, Departamento de Biotecnologia e Produção Vegetal e Animal, Araras, SP, Brazil
| | - Marco Aurélio Takita
- Instituto Agronômico de Campinas, Centro APTA Citros Sylvio Moreira, Cordeirópolis, SP, Brazil
| | | | - Marcos Antonio Machado
- Instituto Agronômico de Campinas, Centro APTA Citros Sylvio Moreira, Cordeirópolis, SP, Brazil
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Fikere M, Barbulescu DM, Malmberg MM, Maharjan P, Salisbury PA, Kant S, Panozzo J, Norton S, Spangenberg GC, Cogan NOI, Daetwyler HD. Genomic Prediction and Genetic Correlation of Agronomic, Blackleg Disease, and Seed Quality Traits in Canola ( Brassica napus L.). PLANTS (BASEL, SWITZERLAND) 2020; 9:E719. [PMID: 32517116 PMCID: PMC7356366 DOI: 10.3390/plants9060719] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 05/29/2020] [Accepted: 06/02/2020] [Indexed: 02/02/2023]
Abstract
Genomic selection accelerates genetic progress in crop breeding through the prediction of future phenotypes of selection candidates based on only their genomic information. Here we report genetic correlations and genomic prediction accuracies in 22 agronomic, disease, and seed quality traits measured across multiple years (2015-2017) in replicated trials under rain-fed and irrigated conditions in Victoria, Australia. Two hundred and two spring canola lines were genotyped for 62,082 Single Nucleotide Polymorphisms (SNPs) using transcriptomic genotype-by-sequencing (GBSt). Traits were evaluated in single trait and bivariate genomic best linear unbiased prediction (GBLUP) models and cross-validation. GBLUP were also expanded to include genotype-by-environment G × E interactions. Genomic heritability varied from 0.31to 0.66. Genetic correlations were highly positive within traits across locations and years. Oil content was positively correlated with most agronomic traits. Strong, not previously documented, negative correlations were observed between average internal infection (a measure of blackleg disease) and arachidic and stearic acids. The genetic correlations between fatty acid traits followed the expected patterns based on oil biosynthesis pathways. Genomic prediction accuracy ranged from 0.29 for emergence count to 0.69 for seed yield. The incorporation of G × E translates into improved prediction accuracy by up to 6%. The genomic prediction accuracies achieved indicate that genomic selection is ready for application in canola breeding.
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Affiliation(s)
- Mulusew Fikere
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC 3086, Australia; (M.F.); (M.M.M.); (G.C.S.); (N.O.I.C.)
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC 3083, Australia;
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), The University of Queensland, Brisbane, QLD 4072, Australia
| | - Denise M. Barbulescu
- Agriculture Victoria, Grains Innovation Park, Horsham, VIC 3400, Australia; (D.M.B.); (P.M.); (S.K.); (J.P.); (S.N.)
| | - M. Michelle Malmberg
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC 3086, Australia; (M.F.); (M.M.M.); (G.C.S.); (N.O.I.C.)
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC 3083, Australia;
| | - Pankaj Maharjan
- Agriculture Victoria, Grains Innovation Park, Horsham, VIC 3400, Australia; (D.M.B.); (P.M.); (S.K.); (J.P.); (S.N.)
| | - Phillip A. Salisbury
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC 3083, Australia;
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Surya Kant
- Agriculture Victoria, Grains Innovation Park, Horsham, VIC 3400, Australia; (D.M.B.); (P.M.); (S.K.); (J.P.); (S.N.)
- Centre for Agricultural Innovation, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Joe Panozzo
- Agriculture Victoria, Grains Innovation Park, Horsham, VIC 3400, Australia; (D.M.B.); (P.M.); (S.K.); (J.P.); (S.N.)
- Centre for Agricultural Innovation, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Sally Norton
- Agriculture Victoria, Grains Innovation Park, Horsham, VIC 3400, Australia; (D.M.B.); (P.M.); (S.K.); (J.P.); (S.N.)
| | - German C. Spangenberg
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC 3086, Australia; (M.F.); (M.M.M.); (G.C.S.); (N.O.I.C.)
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC 3083, Australia;
| | - Noel O. I. Cogan
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC 3086, Australia; (M.F.); (M.M.M.); (G.C.S.); (N.O.I.C.)
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC 3083, Australia;
| | - Hans D. Daetwyler
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC 3086, Australia; (M.F.); (M.M.M.); (G.C.S.); (N.O.I.C.)
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC 3083, Australia;
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Ali F, Nadeem MA, Barut M, Habyarimana E, Chaudhary HJ, Khalil IH, Alsaleh A, Hatipoğlu R, Karaköy T, Kurt C, Aasim M, Sameeullah M, Ludidi N, Yang SH, Chung G, Baloch FS. Genetic Diversity, Population Structure and Marker-Trait Association for 100-Seed Weight in International Safflower Panel Using SilicoDArT Marker Information. PLANTS (BASEL, SWITZERLAND) 2020; 9:E652. [PMID: 32455816 PMCID: PMC7284372 DOI: 10.3390/plants9050652] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 05/18/2020] [Accepted: 05/19/2020] [Indexed: 01/09/2023]
Abstract
Safflower is an important oilseed crop mainly grown in the arid and semi-arid regions of the world. The aim of this study was to explore phenotypic and genetic diversity, population structure, and marker-trait association for 100-seed weight in 94 safflower accessions originating from 26 countries using silicoDArT markers. Analysis of variance revealed statistically significant genotypic effects (p < 0.01), while Turkey samples resulted in higher 100-seed weight compared to Pakistan samples. A Constellation plot divided the studied germplasm into two populations on the basis of their 100-seed weight. Various mean genetic diversity parameters including observed number of alleles (1.99), effective number of alleles (1.54), Shannon's information index (0.48), expected heterozygosity (0.32), and unbiased expected heterozygosity (0.32) for the entire population exhibited sufficient genetic diversity using 12232 silicoDArT markers. Analysis of molecular variance (AMOVA) revealed that most of the variations (91%) in world safflower panel are due to differences within country groups. A model-based structure grouped the 94 safflower accessions into populations A, B, C and an admixture population upon membership coefficient. Neighbor joining analysis grouped the safflower accessions into two populations (A and B). Principal coordinate analysis (PCoA) also clustered the safflower accessions on the basis of geographical origin. Three accessions; Egypt-5, Egypt-2, and India-2 revealed the highest genetic distance and hence might be recommended as candidate parental lines for safflower breeding programs. The mixed linear model i.e., the Q + K model, demonstrated that two DArTseq markers (DArT-45483051 and DArT-15672391) had significant association (p < 0.01) for 100-seed weight. We envisage that identified DArTseq markers associated with 100-seed weight will be helpful to develop high-yielding cultivars of safflower through marker-assisted breeding in the near future.
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Affiliation(s)
- Fawad Ali
- Department of Plant Sciences, Quaid-I-Azam University, Islamabad 45320, Pakistan; (F.A.); (H.J.C.)
- Department of Field Crops, Faculty of Agriculture and Natural Science, Bolu Abant Izzet Baysal University, 14030 Bolu, Turkey; (M.B.); (M.S.)
| | - Muhammad Azhar Nadeem
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, 58140 Sivas, Turkey; (M.A.N.); (T.K.); (M.A.)
| | - Muzaffer Barut
- Department of Field Crops, Faculty of Agriculture and Natural Science, Bolu Abant Izzet Baysal University, 14030 Bolu, Turkey; (M.B.); (M.S.)
- Department of Field Crops, Faculty of Agriculture, Çukurova University, 1000 Adana, Turkey; (R.H.); (C.K.)
| | - Ephrem Habyarimana
- CREA Research Center for Cereal and Industrial Crops, 40128 Bologna, Italy;
| | - Hassan Javed Chaudhary
- Department of Plant Sciences, Quaid-I-Azam University, Islamabad 45320, Pakistan; (F.A.); (H.J.C.)
| | - Iftikhar Hussain Khalil
- Department of Plant Breeding and Genetics, The University of Agriculture, Peshawar 25130, Pakistan;
| | - Ahmad Alsaleh
- Science and Technology Application and Research Center (BİLTEM), Yozgat Bozok University, 66900 Yozgat, Turkey;
| | - Rüştü Hatipoğlu
- Department of Field Crops, Faculty of Agriculture, Çukurova University, 1000 Adana, Turkey; (R.H.); (C.K.)
| | - Tolga Karaköy
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, 58140 Sivas, Turkey; (M.A.N.); (T.K.); (M.A.)
| | - Cemal Kurt
- Department of Field Crops, Faculty of Agriculture, Çukurova University, 1000 Adana, Turkey; (R.H.); (C.K.)
| | - Muhammad Aasim
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, 58140 Sivas, Turkey; (M.A.N.); (T.K.); (M.A.)
| | - Muhammad Sameeullah
- Department of Field Crops, Faculty of Agriculture and Natural Science, Bolu Abant Izzet Baysal University, 14030 Bolu, Turkey; (M.B.); (M.S.)
| | - Ndiko Ludidi
- Department of Biotechnology and Center of Excellence in Food Security, University of the Western Cape, Robert Sobukwe Road, Bellville 7530, South Africa;
| | - Seung Hwan Yang
- Department of Biotechnology, Chonnam National University, Chonnam 59626, Korea;
| | - Gyuhwa Chung
- Department of Biotechnology, Chonnam National University, Chonnam 59626, Korea;
| | - Faheem Shehzad Baloch
- Department of Field Crops, Faculty of Agriculture and Natural Science, Bolu Abant Izzet Baysal University, 14030 Bolu, Turkey; (M.B.); (M.S.)
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Barilli E, Carrillo-Perdomo E, Cobos MJ, Kilian A, Carling J, Rubiales D. Identification of potential candidate genes controlling pea aphid tolerance in a Pisum fulvum high-density integrated DArTseq SNP-based genetic map. PEST MANAGEMENT SCIENCE 2020; 76:1731-1742. [PMID: 31758624 DOI: 10.1002/ps.5696] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 11/08/2019] [Accepted: 11/20/2019] [Indexed: 06/10/2023]
Abstract
BACKGROUND Pea (Pisum sativum) is one of the most important temperate grain legumes in the world, and its production is severely constrained by the pea aphid (Acyrthosiphon pisum). Wild relatives, such as P. fulvum, are valuable sources of allelic diversity to improve the genetic resistance of cultivated pea species against A. pisum attack. To unravel the genetic control underlying resistance to the pea aphid attack, a quantitative trait loci (QTL) analysis was performed using the previously developed high density integrated genetic linkage map originated from an intraspecific recombinant inbred line (RIL) population (P. fulvum: IFPI3260 × IFPI3251). RESULTS We accurately evaluated specific resistance responses to pea aphid that allowed the identification, for the first time, of genomic regions that control plant damage and aphid reproduction. Eight QTLs associated with tolerance to pea aphid were identified in LGs I, II, III, IV and V, which individually explained from 17.0% to 51.2% of the phenotypic variation depending on the trait scored, and as a whole from 17.0% to 88.6%. The high density integrated genetic linkage map also allowed the identification of potential candidate genes co-located with the QTLs identified. CONCLUSIONS Our work shows how the survival of P. fulvum after the pea aphid attack depends on the triggering of a multi-component protection strategy that implies a quantitative tolerance. The genomic regions associated with the tolerance responses of P. fulvum during A. pisum infestation have provided six potential candidate genes that could be useful in marker-assisted selection (MAS) and genomic assisted breeding (GAB) after functional validation in the future. © 2019 Society of Chemical Industry.
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Affiliation(s)
| | - Estefanía Carrillo-Perdomo
- Institute for Sustainable Agriculture, CSIC, Córdoba, Spain
- Current address: Agroécologie, AgroSup Dijon, INRAE, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, F-21000 Dijon, France
| | | | - Andrzej Kilian
- Diversity Arrays Technology Pty Ltd, University of Canberra, Canberra, Australia
| | - Jason Carling
- Diversity Arrays Technology Pty Ltd, University of Canberra, Canberra, Australia
| | - Diego Rubiales
- Institute for Sustainable Agriculture, CSIC, Córdoba, Spain
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Ahmar S, Gill RA, Jung KH, Faheem A, Qasim MU, Mubeen M, Zhou W. Conventional and Molecular Techniques from Simple Breeding to Speed Breeding in Crop Plants: Recent Advances and Future Outlook. Int J Mol Sci 2020; 21:E2590. [PMID: 32276445 PMCID: PMC7177917 DOI: 10.3390/ijms21072590] [Citation(s) in RCA: 126] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Revised: 04/03/2020] [Accepted: 04/05/2020] [Indexed: 01/28/2023] Open
Abstract
In most crop breeding programs, the rate of yield increment is insufficient to cope with the increased food demand caused by a rapidly expanding global population. In plant breeding, the development of improved crop varieties is limited by the very long crop duration. Given the many phases of crossing, selection, and testing involved in the production of new plant varieties, it can take one or two decades to create a new cultivar. One possible way of alleviating food scarcity problems and increasing food security is to develop improved plant varieties rapidly. Traditional farming methods practiced since quite some time have decreased the genetic variability of crops. To improve agronomic traits associated with yield, quality, and resistance to biotic and abiotic stresses in crop plants, several conventional and molecular approaches have been used, including genetic selection, mutagenic breeding, somaclonal variations, whole-genome sequence-based approaches, physical maps, and functional genomic tools. However, recent advances in genome editing technology using programmable nucleases, clustered regularly interspaced short palindromic repeats (CRISPR), and CRISPR-associated (Cas) proteins have opened the door to a new plant breeding era. Therefore, to increase the efficiency of crop breeding, plant breeders and researchers around the world are using novel strategies such as speed breeding, genome editing tools, and high-throughput phenotyping. In this review, we summarize recent findings on several aspects of crop breeding to describe the evolution of plant breeding practices, from traditional to modern speed breeding combined with genome editing tools, which aim to produce crop generations with desired traits annually.
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Affiliation(s)
- Sunny Ahmar
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China; (S.A.); (M.U.Q.)
| | - Rafaqat Ali Gill
- Oil Crops Research Institute, Chinese Academy of Agriculture Sciences, Wuhan 430070, China;
| | - Ki-Hong Jung
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin 17104, Korea
| | - Aroosha Faheem
- State Key Laboratory of Agricultural Microbiology and State Key Laboratory of Microbial Biosensor, College of Life Sciences Huazhong Agriculture University, Wuhan 430070, China
| | - Muhammad Uzair Qasim
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China; (S.A.); (M.U.Q.)
| | - Mustansar Mubeen
- State Key Laboratory of Agricultural Microbiology and Provincial Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Weijun Zhou
- Institute of Crop Science and Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou 310058, China
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Martin A, Moolhuijzen P, Tao Y, McIlroy J, Ellwood SR, Fowler RA, Platz GJ, Kilian A, Snyman L. Genomic Regions Associated with Virulence in Pyrenophora teres f. teres Identified by Genome-Wide Association Analysis and Biparental Mapping. PHYTOPATHOLOGY 2020; 110:881-891. [PMID: 31855502 DOI: 10.1094/phyto-10-19-0372-r] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Net form net blotch (NFNB), caused by the fungal pathogen Pyrenophora teres f. teres, is an important foliar disease present in all barley-producing regions of the world. This fungus is a hemibiotrophic and heterothallic ascomycete, where sexual recombination can lead to changes in disease expression in the host. Knowledge of the genetic architecture and genes involved in virulence is vital to increase the durability of NFNB resistance in barley cultivars. We used a genome-wide association mapping approach to characterize P. teres f. teres genomic regions associated with virulence in Australian barley cultivars. One hundred eighty-eight P. teres f. teres isolates collected across five Australian states were genotyped using Diversity Arrays Technology sequence markers and phenotyped across 20 different barley genotypes. Association mapping identified 14 different genomic regions associated with virulence, with the majority located on P. teres f. teres chromosomes 3 and 5 and one each present on chromosomes 1, 6, and 9. Four of the regions identified were confirmed by quantitative trait loci (QTL) mapping. The QTL regions are discussed in the context of their genomic architecture together with examination of their gene contents, which identified 20 predicted effectors. The number of QTL shown in this study at the population level clearly illustrates a complex genetic basis of P. teres f. teres virulence compared with pure necrotrophs, such as the wheat pathogens Parastagonospora nodorum and Parastagonospora tritici-repentis.
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Affiliation(s)
- Anke Martin
- Centre for Crop Health, University of Southern Queensland, Toowoomba, Queensland 4370, Australia
| | - Paula Moolhuijzen
- Centre for Crop & Disease Management, Department of Environment and Agriculture, Curtin University, Bentley, Western Australia 6102, Australia
| | - Yongfu Tao
- Hermitage Research Facility, Department of Agriculture & Fisheries, Warwick, Queensland 4370, Australia
| | - Judy McIlroy
- Hermitage Research Facility, Department of Agriculture & Fisheries, Warwick, Queensland 4370, Australia
| | - Simon R Ellwood
- Centre for Crop & Disease Management, Department of Environment and Agriculture, Curtin University, Bentley, Western Australia 6102, Australia
| | - Ryan A Fowler
- Hermitage Research Facility, Department of Agriculture & Fisheries, Warwick, Queensland 4370, Australia
| | - Greg J Platz
- Hermitage Research Facility, Department of Agriculture & Fisheries, Warwick, Queensland 4370, Australia
| | - Andrzej Kilian
- Diversity Arrays Technology, Bruce, Australian Capital Territory 2617, Australia
| | - Lisle Snyman
- Hermitage Research Facility, Department of Agriculture & Fisheries, Warwick, Queensland 4370, Australia
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Kaur J, Akhatar J, Goyal A, Kaur N, Kaur S, Mittal M, Kumar N, Sharma H, Banga S, Banga SS. Genome wide association mapping and candidate gene analysis for pod shatter resistance in Brassica juncea and its progenitor species. Mol Biol Rep 2020; 47:2963-2974. [PMID: 32219770 DOI: 10.1007/s11033-020-05384-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 03/19/2020] [Indexed: 01/07/2023]
Abstract
We investigated phenotypic variations for pod shattering, pod length and number of seeds per pod in large germplasm collections of Brassica juncea (2n = 36; AABB) and its progenitor species, B. rapa (2n = 20; AA) and B. nigra (2n = 16; BB). Pod shatter resistance was measured as energy required for rupturing a mature dry pod, with a specially fabricated pendulum machine. Rupture energy (RE) ranged from 3.3 to 11.0 mJ in B. juncea. MCP 633, NR 3350 and Albeli required maximum energy to shatter a pod. It ranged from 2.5 to 7.8 mJ for B. rapa with an average of 5.5 mJ. B. nigra possessed easy to rupture pods. Correlation analysis showed strong associations among these traits in B. juncea and B. rapa. Genome wide association studies were conducted with select sets of B. juncea and B. rapa germplasm lines. Significant and annotated associations predict the role of FRUITFULL, MANNASE7, and NAC secondary wall thickening promoting factor (NST2) in the genetic regulation of shatter resistance in B. juncea. NST2 and SHP1 appeared important for pod length and seeds per pod in B. rapa. Candidate gene based association mapping also confirmed the role of SHP1 and NST2 in regulating pod shattering and related pod traits in B. rapa and B. juncea. Footprints of selection were detected in SHP1, SHP2 (B. rapa, B. nigra and B. juncea), RPL (B. rapa) and NAC (B. juncea). Our results provide insights into the genetic architecture of three pod traits. The identified genes are relevant to improving and securing crop productivity of mustard crop.
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Affiliation(s)
- Jasmeet Kaur
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Javed Akhatar
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Anna Goyal
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Navneet Kaur
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Snehdeep Kaur
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Meenakshi Mittal
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Nitin Kumar
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Heena Sharma
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Shashi Banga
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - S S Banga
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India.
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Genetic and physical mapping of loci for resistance to blackleg disease in canola (Brassica napus L.). Sci Rep 2020; 10:4416. [PMID: 32157120 PMCID: PMC7064481 DOI: 10.1038/s41598-020-61211-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 02/19/2020] [Indexed: 01/10/2023] Open
Abstract
Sustainable canola production is essential to meet growing human demands for vegetable oil, biodiesel, and meal for stock feed markets. Blackleg, caused by the fungal pathogen, Leptosphaeria maculans is a devastating disease that can lead to significant yield loss in many canola production regions worldwide. Breakdown of race-specific resistance to L. maculans in commercial cultivars poses a constant threat to the canola industry. To identify new alleles, especially for quantitative resistance (QR), we analyzed 177 doubled haploid (DH) lines derived from an RP04/Ag-Outback cross. DH lines were evaluated for QR under field conditions in three experiments conducted at Wagga Wagga (2013, 2014) and Lake Green (2015), and under shade house conditions using the 'ascospore shower' test. DH lines were also characterized for qualitative R gene-mediated resistance via cotyledon tests with two differential single spore isolates, IBCN17 and IBCN76, under glasshouse conditions. Based on 18,851 DArTseq markers, a linkage map representing 2,019 unique marker bins was constructed and then utilized for QTL detection. Marker regression analysis identified 22 significant marker associations for resistance, allowing identification of two race-specific resistance R genes, Rlm3 and Rlm4, and 21 marker associations for QR loci. At least three SNP associations for QR were repeatedly detected on chromosomes A03, A07 and C04 across phenotyping environments. Physical mapping of markers linked with these consistent QR loci on the B. napus genome assembly revealed their localization in close proximity of the candidate genes of B. napus BnaA03g26760D (A03), BnaA07g20240D (A07) and BnaC04g02040D (C04). Annotation of these candidate genes revealed their association with protein kinase and jumonji proteins implicated in defense resistance. Both Rlm3 and Rlm4 genes identified in this DH population did not show any association with resistance loci detected under either field and/or shade house conditions (ascospore shower) suggesting that both genes are ineffective in conferring resistance to L. maculans in Australian field conditions. Taken together, our study identified sequence-based molecular markers for dissecting R and QR loci to L. maculans in a canola DH population from the RP04/Ag-Outback cross.
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Aznar-Fernández T, Barilli E, Cobos MJ, Kilian A, Carling J, Rubiales D. Identification of quantitative trait loci (QTL) controlling resistance to pea weevil (Bruchus pisorum) in a high-density integrated DArTseq SNP-based genetic map of pea. Sci Rep 2020; 10:33. [PMID: 31913335 PMCID: PMC6949260 DOI: 10.1038/s41598-019-56987-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 12/19/2019] [Indexed: 12/22/2022] Open
Abstract
Pea weevil (Bruchus pisorum) is a damaging insect pest affecting pea (Pisum sativum) production worldwide. No resistant cultivars are available, although some levels of incomplete resistance have been identified in Pisum germplasm. To decipher the genetic control underlying the resistance previously identify in P. sativum ssp. syriacum, a recombinant inbred line (RIL F8:9) population was developed. The RIL was genotyped through Diversity Arrays Technology PL's DArTseq platform and screened under field conditions for weevil seed infestation and larval development along 5 environments. A newly integrated genetic linkage map was generated with a subset of 6,540 markers, assembled into seven linkage groups, equivalent to the number of haploid pea chromosomes. An accumulated distance of 2,503 cM was covered with an average density of 2.61 markers cM-1. The linkage map allowed the identification of three QTLs associated to reduced seed infestation along LGs I, II and IV. In addition, a QTL for reduced larval development was also identified in LGIV. Expression of these QTLs varied with the environment, being particularly interesting QTL BpSI.III that was detected in most of the environments studied. This high-saturated pea genetic map has also allowed the identification of seven potential candidate genes co-located with QTLs for marker-assisted selection, providing an opportunity for breeders to generate effective and sustainable strategies for weevil control.
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Affiliation(s)
| | - Eleonora Barilli
- Institute for Sustainable Agriculture, CSIC, Córdoba, E-14004, Spain.
| | - María J Cobos
- Institute for Sustainable Agriculture, CSIC, Córdoba, E-14004, Spain
| | - Andrzej Kilian
- Diversity Arrays Technology Pty Ltd, University of Canberra, Kirinari St. Bruce, ACT2617, Australia
| | - Jason Carling
- Diversity Arrays Technology Pty Ltd, University of Canberra, Kirinari St. Bruce, ACT2617, Australia
| | - Diego Rubiales
- Institute for Sustainable Agriculture, CSIC, Córdoba, E-14004, Spain
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Stephenson P, Stacey N, Brüser M, Pullen N, Ilyas M, O'Neill C, Wells R, Østergaard L. The power of model-to-crop translation illustrated by reducing seed loss from pod shatter in oilseed rape. PLANT REPRODUCTION 2019; 32:331-340. [PMID: 31222677 PMCID: PMC6820617 DOI: 10.1007/s00497-019-00374-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 06/14/2019] [Indexed: 05/17/2023]
Abstract
Elucidation of key regulators in Arabidopsis fruit patterning has facilitated knowledge-translation into crop species to address yield loss caused by premature seed dispersal (pod shatter). In the 1980s, plant scientists descended on a small weed Arabidopsis thaliana (thale cress) and developed it into a powerful model system to study plant biology. The massive advances in genetics and genomics since then have allowed us to obtain incredibly detailed knowledge on specific biological processes of Arabidopsis growth and development, its genome sequence and the function of many of the individual genes. This wealth of information provides immense potential for translation into crops to improve their performance and address issues of global importance such as food security. Here, we describe how fundamental insight into the genetic mechanism by which seed dispersal occurs in members of the Brassicaceae family can be exploited to reduce seed loss in oilseed rape (Brassica napus). We demonstrate that by exploiting data on gene function in model species, it is possible to adjust the pod-opening process in oilseed rape, thereby significantly increasing yield. Specifically, we identified mutations in multiple paralogues of the INDEHISCENT and GA4 genes in B. napus and have overcome genetic redundancy by combining mutant alleles. Finally, we present novel software for the analysis of pod shatter data that is applicable to any crop for which seed dispersal is a serious problem. These findings highlight the tremendous potential of fundamental research in guiding strategies for crop improvement.
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Affiliation(s)
- Pauline Stephenson
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Nicola Stacey
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Marie Brüser
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
- , London, UK
| | - Nick Pullen
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Muhammad Ilyas
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
- Department of Biological Sciences, Faculty of Basic and Applied Science, International Islamic University, Islamabad, Pakistan
| | - Carmel O'Neill
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Rachel Wells
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Lars Østergaard
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK.
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Zaman QU, Chu W, Hao M, Shi Y, Sun M, Sang SF, Mei D, Cheng H, Liu J, Li C, Hu Q. CRISPR/Cas9-Mediated Multiplex Genome Editing of JAGGED Gene in Brassica napus L. Biomolecules 2019; 9:biom9110725. [PMID: 31726660 PMCID: PMC6921047 DOI: 10.3390/biom9110725] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 11/07/2019] [Indexed: 11/16/2022] Open
Abstract
Pod shattering resistance is an essential component to achieving a high yield, which is a substantial objective in polyploid rapeseed cultivation. Previous studies have suggested that the Arabidopsis JAGGED (JAG) gene is a key factor implicated in the regulatory web of dehiscence fruit. However, its role in controlling pod shattering resistance in oilseed rape is still unknown. In this study, multiplex genome editing was carried out by the CRISPR/Cas9 system on five homoeologs (BnJAG.A02, BnJAG.C02, BnJAG.C06, BnJAG.A07, and BnJAG.A08) of the JAG gene. Knockout mutagenesis of all homoeologs drastically affected the development of the lateral organs in organizing pod shape and size. The cylindrical body of the pod comprised a number of undifferentiated cells like a callus, without distinctive valves, replum, septum, and valve margins. Pseudoseeds were produced, which were divided into two halves with an incomplete layer of cells (probably septum) that separated the undifferentiated cells. These mutants were not capable of generating any productive seeds for further generations. However, one mutant line was identified in which only a BnJAG.A08-NUB-Like paralog of the JAG gene was mutated. Knockout mutagenesis in BnJAG.A08-NUB gene caused significant changes in the pod dehiscence zone. The replum region of the mutant was increased to a great extent, resulting in enlarged cell size, bumpy fruit, and reduced length compared with the wild type. A higher replum-valve joint area may have increased the resistance to pod shattering by ~2-fold in JAG mutants compared with wild type. Our results offer a basis for understanding variations in Brassica napus fruit by mutating JAG genes and providing a way forward for other Brassicaceae species.
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Affiliation(s)
- Qamar U Zaman
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Key Laboratory for Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, No. 2 Xudong 2nd Road, Wuhan 430062, China; (Q.U.Z.); (W.C.); (M.H.); (Y.S.); (M.S.); (S.-F.S.); (D.M.); (H.C.); (J.L.)
- Graduate School of Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Wen Chu
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Key Laboratory for Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, No. 2 Xudong 2nd Road, Wuhan 430062, China; (Q.U.Z.); (W.C.); (M.H.); (Y.S.); (M.S.); (S.-F.S.); (D.M.); (H.C.); (J.L.)
| | - Mengyu Hao
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Key Laboratory for Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, No. 2 Xudong 2nd Road, Wuhan 430062, China; (Q.U.Z.); (W.C.); (M.H.); (Y.S.); (M.S.); (S.-F.S.); (D.M.); (H.C.); (J.L.)
| | - Yuqin Shi
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Key Laboratory for Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, No. 2 Xudong 2nd Road, Wuhan 430062, China; (Q.U.Z.); (W.C.); (M.H.); (Y.S.); (M.S.); (S.-F.S.); (D.M.); (H.C.); (J.L.)
| | - Mengdan Sun
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Key Laboratory for Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, No. 2 Xudong 2nd Road, Wuhan 430062, China; (Q.U.Z.); (W.C.); (M.H.); (Y.S.); (M.S.); (S.-F.S.); (D.M.); (H.C.); (J.L.)
| | - Shi-Fei Sang
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Key Laboratory for Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, No. 2 Xudong 2nd Road, Wuhan 430062, China; (Q.U.Z.); (W.C.); (M.H.); (Y.S.); (M.S.); (S.-F.S.); (D.M.); (H.C.); (J.L.)
| | - Desheng Mei
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Key Laboratory for Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, No. 2 Xudong 2nd Road, Wuhan 430062, China; (Q.U.Z.); (W.C.); (M.H.); (Y.S.); (M.S.); (S.-F.S.); (D.M.); (H.C.); (J.L.)
| | - Hongtao Cheng
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Key Laboratory for Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, No. 2 Xudong 2nd Road, Wuhan 430062, China; (Q.U.Z.); (W.C.); (M.H.); (Y.S.); (M.S.); (S.-F.S.); (D.M.); (H.C.); (J.L.)
| | - Jia Liu
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Key Laboratory for Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, No. 2 Xudong 2nd Road, Wuhan 430062, China; (Q.U.Z.); (W.C.); (M.H.); (Y.S.); (M.S.); (S.-F.S.); (D.M.); (H.C.); (J.L.)
| | - Chao Li
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Key Laboratory for Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, No. 2 Xudong 2nd Road, Wuhan 430062, China; (Q.U.Z.); (W.C.); (M.H.); (Y.S.); (M.S.); (S.-F.S.); (D.M.); (H.C.); (J.L.)
- Correspondence: (C.L.); (Q.H.)
| | - Qiong Hu
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Key Laboratory for Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, No. 2 Xudong 2nd Road, Wuhan 430062, China; (Q.U.Z.); (W.C.); (M.H.); (Y.S.); (M.S.); (S.-F.S.); (D.M.); (H.C.); (J.L.)
- Correspondence: (C.L.); (Q.H.)
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