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Sunflower Genetics
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Sunflower Genetics

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Plant Genetics and Genomics".

Deadline for manuscript submissions: closed (17 January 2020) | Viewed by 35415

Special Issue Editors

Dr. Rose L. Andrew

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Guest Editor
University of New England Australia, Armidale, Australia
Dr. Michael Kantar

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Co-Guest Editor
Tropical Plant & Soil Sciences, University of Hawaii at Manoa, 2500 Campus Road, Honolulu, HI 96822, USA
Interests: using techniques from genetics, genomics, plant breeding, ecology, geography, and agroecology to develop new crops and improve old ones for a changing environment
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Sunflowers in the genus Helianthus are important crops that produce a range of products, including oil, seeds, tubers and cut flowers. Domesticated sunflowers have diverse wild relatives, with many potentially useful traits for breeding resilient crops in changing abiotic and biotic environments, especially disease resistance. The availability of a reference genome is now helping researchers to unpack the biotic interactions, climate adaptation, and evolutionary history of sunflowers.

This Special Issue on ‘’Sunflower Genetics’’ aims to document the cutting edge of applied and basic research on sunflower genetics globally, bringing together research developments making use of the sunflower reference genome and related technologies. We seek papers using population genomics and molecular genetics, particularly those addressing molecular and evolutionary mechanisms. The focus is on Helianthus annuus and other species within the genus, including wild, weedy, and domesticated forms, with the goal of representing the diversity of authors and regions involved in research on sunflower genetics. 

Dr. Rose L. Andrew
Dr. Michael Kantar
Guest Editors

Manuscript Submission Information

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Keywords

  • Helianthus
  • sunflower
  • genetic improvement
  • population genomics
  • hybridisation
  • adaptation
  • diversification.

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Published Papers (7 papers)

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Research

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21 pages, 13176 KiB  
Article
Genome-Wide Identification and Analysis of P-Type Plasma Membrane H+-ATPase Sub-Gene Family in Sunflower and the Role of HHA4 and HHA11 in the Development of Salt Stress Resistance
by Zongchang Xu, Prince Marowa, Han Liu, Haina Du, Chengsheng Zhang and Yiqiang Li
Genes 2020, 11(4), 361; https://doi.org/10.3390/genes11040361 - 27 Mar 2020
Cited by 16 | Viewed by 3984
Abstract
The P-type plasma membrane (PM) H+-ATPase plays a major role during the growth and development of a plant. It is also involved in plant resistance to a variety of biotic and abiotic factors, including salt stress. The PM H+-ATPase [...] Read more.
The P-type plasma membrane (PM) H+-ATPase plays a major role during the growth and development of a plant. It is also involved in plant resistance to a variety of biotic and abiotic factors, including salt stress. The PM H+-ATPase gene family has been well characterized in Arabidopsis and other crop plants such as rice, cucumber, and potato; however, the same cannot be said in sunflower (Helianthus annuus). In this study, a total of thirteen PM H+-ATPase genes were screened from the recently released sunflower genome database with a comprehensive genome-wide analysis. According to a systematic phylogenetic classification with a previously reported species, the sunflower PM H+-ATPase genes (HHAs) were divided into four sub-clusters (I, II, IV, and V). In addition, systematic bioinformatics analyses such as gene structure analysis, chromosome location analysis, subcellular localization predication, conserved motifs, and Cis-acting elements of promoter identification were also done. Semi-quantitative PCR analysis data of HHAs in different sunflower tissues revealed the specificity of gene spatiotemporal expression and sub-cluster grouping. Those belonging to sub-cluster I and II exhibited wide expression in almost all of the tissues studied while sub-cluster IV and V seldom showed expression. In addition, the expression of HHA4, HHA11, and HHA13 was shown to be induced by salt stress. The transgenic plants overexpressing HHA4 and HHA11 showed higher salinity tolerance compared with wild-type plants. Further analysis showed that the Na+ content of transgenic Arabidopsis plants decreased under salt stress, which indicates that PM H+ ATPase participates in the physiological process of Na+ efflux, resulting in salt resistance of the plants. This study is the first to identify and analyze the sunflower PM H+ ATPase gene family. It does not only lay foundation for future research but also demonstrates the role played by HHAs in salt stress tolerance. Full article
(This article belongs to the Special Issue Sunflower Genetics)
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15 pages, 3581 KiB  
Article
Genetic Diversity, Population Structure and Linkage Disequilibrium Assessment among International Sunflower Breeding Collections
by Carla V. Filippi, Gabriela A. Merino, Juan F. Montecchia, Natalia C. Aguirre, Máximo Rivarola, Guy Naamati, Mónica I. Fass, Daniel Álvarez, Julio Di Rienzo, Ruth A. Heinz, Bruno Contreras Moreira, Verónica V. Lia and Norma B. Paniego
Genes 2020, 11(3), 283; https://doi.org/10.3390/genes11030283 - 6 Mar 2020
Cited by 18 | Viewed by 5499
Abstract
Sunflower germplasm collections are valuable resources for broadening the genetic base of commercial hybrids and ameliorate the risk of climate events. Nowadays, the most studied worldwide sunflower pre-breeding collections belong to INTA (Argentina), INRA (France), and USDA-UBC (United States of America–Canada). In this [...] Read more.
Sunflower germplasm collections are valuable resources for broadening the genetic base of commercial hybrids and ameliorate the risk of climate events. Nowadays, the most studied worldwide sunflower pre-breeding collections belong to INTA (Argentina), INRA (France), and USDA-UBC (United States of America–Canada). In this work, we assess the amount and distribution of genetic diversity (GD) available within and between these collections to estimate the distribution pattern of global diversity. A mixed genotyping strategy was implemented, by combining proprietary genotyping-by-sequencing data with public whole-genome-sequencing data, to generate an integrative 11,834-common single nucleotide polymorphism matrix including the three breeding collections. In general, the GD estimates obtained were moderate. An analysis of molecular variance provided evidence of population structure between breeding collections. However, the optimal number of subpopulations, studied via discriminant analysis of principal components (K = 12), the bayesian STRUCTURE algorithm (K = 6) and distance-based methods (K = 9) remains unclear, since no single unifying characteristic is apparent for any of the inferred groups. Different overall patterns of linkage disequilibrium (LD) were observed across chromosomes, with Chr10, Chr17, Chr5, and Chr2 showing the highest LD. This work represents the largest and most comprehensive inter-breeding collection analysis of genomic diversity for cultivated sunflower conducted to date. Full article
(This article belongs to the Special Issue Sunflower Genetics)
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14 pages, 2256 KiB  
Article
Mapping of the New Fertility Restorer Gene Rf-PET2 Close to Rf1 on Linkage Group 13 in Sunflower (Helianthus annuus L.)
by Osama Sajer, Uta Schirmak, Sonia Hamrit and Renate Horn
Genes 2020, 11(3), 269; https://doi.org/10.3390/genes11030269 - 1 Mar 2020
Cited by 6 | Viewed by 3758
Abstract
The PET2-cytoplasm represents a well characterized new source of cytoplasmic male sterility (CMS) in sunflower. It is distinct from the PET1-cytoplasm, used worldwide for commercial hybrid breeding, although it was, as PET1, derived from an interspecific cross between Helianthus. petiolaris and H. annuus [...] Read more.
The PET2-cytoplasm represents a well characterized new source of cytoplasmic male sterility (CMS) in sunflower. It is distinct from the PET1-cytoplasm, used worldwide for commercial hybrid breeding, although it was, as PET1, derived from an interspecific cross between Helianthus. petiolaris and H. annuus. Fertility restoration is essential for the use of CMS PET2 in sunflower hybrid breeding. Markers closely linked to the fertility restorer gene are needed to build up a pool of restorer lines. Fertility-restored F1-hybrids RHA 265(PET2) × IH-51 showed pollen viability of 98.2% ± 1.2, indicating a sporophytic mode of fertility restoration. Segregation analyses in the F2-population of the cross RHA 265(PET2) × IH-51 revealed that this cross segregated for one major restorer gene Rf-PET2. Bulked-segregant analyses investigating 256 amplified fragment length polymorphism (AFLP) primer combinations revealed a high degree of polymorphism in this cross. Using a subset of 24 AFLP markers, three sequence-tagged site (STS) markers and three microsatellite markers, Rf-PET2 could be mapped to the distal region of linkage group 13 between ORS1030 and ORS630. Three AFLP markers linked to Rf-PET2 were cloned and sequenced. Homology search against the sunflower genome sequence of HanXRQ v1r1 confirmed the physical location of Rf-PET2 close to the restorer gene Rf1 for CMS PET1. STS markers were mapped that can now be used for marker-assisted selection. Full article
(This article belongs to the Special Issue Sunflower Genetics)
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18 pages, 1934 KiB  
Article
Phylogeography and the Evolutionary History of Sunflower (Helianthus annuus L.): Wild Diversity and the Dynamics of Domestication
by Brian Park and John M. Burke
Genes 2020, 11(3), 266; https://doi.org/10.3390/genes11030266 - 29 Feb 2020
Cited by 11 | Viewed by 6775
Abstract
Patterns of genetic variation in crops are the result of selection and demographic changes that occurred during their domestication and improvement. In many cases, we have an incomplete picture of the origin of crops in the context of their wild progenitors, particularly with [...] Read more.
Patterns of genetic variation in crops are the result of selection and demographic changes that occurred during their domestication and improvement. In many cases, we have an incomplete picture of the origin of crops in the context of their wild progenitors, particularly with regard to the processes producing observed levels of standing genetic variation. Here, we analyzed sequence diversity in cultivated sunflower (Helianthus annuus L.) and its wild progenitor (common sunflower, also H. annuus) to reconstruct phylogeographic relationships and population genetic/demographic patterns across sunflower. In common sunflower, south-north patterns in the distribution of nucleotide diversity and lineage splitting indicate a history of rapid postglacial range expansion from southern refugia. Cultivated sunflower accessions formed a clade, nested among wild populations from the Great Plains, confirming a single domestication event in central North America. Furthermore, cultivated accessions sorted by market type (i.e., oilseed vs. confectionery) rather than breeding pool, recapitulating the secondary development of oil-rich cultivars during its breeding history. Across sunflower, estimates of nucleotide diversity and effective population sizes suggest that cultivated sunflower underwent significant population bottlenecks following its establishment ~5000 years ago. The patterns inferred here corroborate those from previous studies of sunflower domestication, and provide a comprehensive overview of its evolutionary history. Full article
(This article belongs to the Special Issue Sunflower Genetics)
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14 pages, 1200 KiB  
Article
Marker-Assisted Gene Pyramiding and the Reliability of Using SNP Markers Located in the Recombination Suppressed Regions of Sunflower (Helianthus annuus L.)
by Lili Qi and Guojia Ma
Genes 2020, 11(1), 10; https://doi.org/10.3390/genes11010010 - 20 Dec 2019
Cited by 21 | Viewed by 3830
Abstract
Rust caused by the fungus Puccinia helianthi and downy mildew (DM) caused by the obligate pathogen Plasmopara halstedii are two of the most globally important sunflower diseases. Resistance to rust and DM is controlled by race-specific single dominant genes. The present study aimed [...] Read more.
Rust caused by the fungus Puccinia helianthi and downy mildew (DM) caused by the obligate pathogen Plasmopara halstedii are two of the most globally important sunflower diseases. Resistance to rust and DM is controlled by race-specific single dominant genes. The present study aimed at pyramiding rust resistance genes combined with a DM resistance gene, using molecular markers. Four rust resistant lines, HA-R3 (carrying the R4 gene), HA-R2 (R5), HA-R8 (R15), and RHA 397 (R13b), were each crossed with a common line, RHA 464, carrying a rust gene R12 and a DM gene PlArg. An additional cross was made between HA-R8 and RHA 397. Co-dominant simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers linked to the target genes were used to discriminate between homozygotes and heterozygotes in F2 populations. Five pyramids with different combinations of rust resistance genes were selected in the homozygous condition through marker-assisted selection, and three of them were combined with a DM resistance gene PlArg: R4/R12/PlArg, R5/R12/PlArg, R13b/R12/PlArg, R15/R12, and R13b/R15. The pyramiding lines with the stacking of two rust and one DM genes were resistant to all known races of North American sunflower rust and all known races of the pathogen causing DM, potentially providing multiple and durable resistance to both rust and DM. A cluster of 12 SNP markers spanning a region of 34.5 Mb on chromosome 1, which co-segregate with PlArg, were tested in four populations. Use of those markers, located in a recombination suppressed region in marker selection, is discussed. Full article
(This article belongs to the Special Issue Sunflower Genetics)
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12 pages, 2252 KiB  
Article
Skim-Sequencing Reveals the Likely Origin of the Enigmatic Endangered Sunflower Helianthus schweinitzii
by Justin Anderson, Michael Kantar, Dan Bock, Kunsiri Chaw Grubbs, Edward Schilling and Loren Rieseberg
Genes 2019, 10(12), 1040; https://doi.org/10.3390/genes10121040 - 15 Dec 2019
Cited by 2 | Viewed by 3541
Abstract
Resolving the origin of endangered taxa is an essential component of conservation. This information can be used to guide efforts of bolstering genetic diversity, and also enables species recovery and future evolutionary studies. Here, we used low-coverage whole genome sequencing to clarify the [...] Read more.
Resolving the origin of endangered taxa is an essential component of conservation. This information can be used to guide efforts of bolstering genetic diversity, and also enables species recovery and future evolutionary studies. Here, we used low-coverage whole genome sequencing to clarify the origin of Helianthus schweinitzii, an endangered tetraploid sunflower that is endemic to the Piedmont Plateau in the eastern United States. We surveyed four accessions representing four populations of H. schweinitzii and 38 accessions of six purported parental species. Using de novo approaches, we assembled 87,004 bp of the chloroplast genome and 6770 bp of the nuclear 35S rDNA. Phylogenetic reconstructions based on the chloroplast genome revealed no reciprocal monophyly of taxa. In contrast, nuclear rDNA data strongly supported the currently accepted sections of the genus Helianthus. Information from combined cpDNA and rDNA provided evidence that H. schweinitzii is likely an allo-tetraploid that formed as a result of hybridization between the diploids Helianthus giganteus and Helianthus microcephalus. Full article
(This article belongs to the Special Issue Sunflower Genetics)
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Review

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17 pages, 758 KiB  
Review
Genetic and Genomic Tools in Sunflower Breeding for Broomrape Resistance
by Sandra Cvejić, Aleksandra Radanović, Boško Dedić, Milan Jocković, Siniša Jocić and Dragana Miladinović
Genes 2020, 11(2), 152; https://doi.org/10.3390/genes11020152 - 30 Jan 2020
Cited by 31 | Viewed by 7151
Abstract
Broomrape is a root parasitic plant causing yield losses in sunflower production. Since sunflower is an important oil crop, the development of broomrape-resistant hybrids is the prime breeding objective. Using conventional plant breeding methods, breeders have identified resistant genes and developed a number [...] Read more.
Broomrape is a root parasitic plant causing yield losses in sunflower production. Since sunflower is an important oil crop, the development of broomrape-resistant hybrids is the prime breeding objective. Using conventional plant breeding methods, breeders have identified resistant genes and developed a number of hybrids resistant to broomrape, adapted to different growing regions worldwide. However, the spread of broomrape into new countries and the development of new and more virulent races have been noted intensively. Recent advances in sunflower genomics provide additional tools for plant breeders to improve resistance and find durable solutions for broomrape spread and virulence. This review describes the structure and distribution of new, virulent physiological broomrape races, sources of resistance for introduction into susceptible cultivated sunflower, qualitative and quantitative resistance genes along with gene pyramiding and marker assisted selection (MAS) strategies applied in the process of increasing sunflower resistance. In addition, it presents an overview of underutilized biotechnological tools, such as phenotyping, -omics, and genome editing techniques, which need to be introduced in the study of sunflower resistance to broomrape in order to achieve durable resistance. Full article
(This article belongs to the Special Issue Sunflower Genetics)
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