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Lee SR. Adaptive divergence for a drought resistance related trait among invasive Saltcedar ( Tamarix L.) populations in southwestern US: Inferences from QCT - FCT. FRONTIERS IN PLANT SCIENCE 2022; 13:997805. [PMID: 36452108 PMCID: PMC9702568 DOI: 10.3389/fpls.2022.997805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 10/20/2022] [Indexed: 06/17/2023]
Abstract
Biological invasion poses several biotic and abiotic challenges due to abrupt distribution shifts. Invasive species may benefit from local adaptation responding to environmental stresses during colonization. Saltcedar (Tamarix), a notorious invasive shrub in the western US introduced from Eurasia may have adapted to low rainfall as the species widely occupies the arid land throughout the southwestern US. We investigated variation of quantitative traits in saltcedar between two regions exhibiting opposing average annual precipitations under experimentally manipulated water treatments to test local adaptation. We measured eight quantitative traits, proxies for fitness and genotyped 64 individual samples using genotype by sequencing technique. To test local adaptation, we applied QCT - FCT test based on null distribution of FCT estimated from 2,697 genome-wide SNPs and QCT estimated for the eight phenotypic traits measured. Saltcedar in the southwestern US exhibited a significant interaction between the degree of leaf loss (biomass loss by senesced leaves to total biomass) under simulated drought conditions and the origins from which the genotypes were collected, either relatively high or low rainfall regimes. The divergence found in leaf loss was significantly greater among regions than the expected given the genetic divergence on neutral loci suggesting signature of local adaptation responding to drought. The results demonstrate adaptive potential of saltcedar populations to extreme drought. As extreme aridity is often predicted in climate models across the southwestern US, the western saltcedar genotypes locally adapted to drought may further expand their ranges in this region.
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Maina F, Harou A, Hamidou F, Morris GP. Genome-wide association studies identify putative pleiotropic locus mediating drought tolerance in sorghum. PLANT DIRECT 2022; 6:e413. [PMID: 35774626 PMCID: PMC9219007 DOI: 10.1002/pld3.413] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 05/17/2022] [Accepted: 05/28/2022] [Indexed: 06/01/2023]
Abstract
Drought is a key constraint on plant productivity and threat to food security. Sorghum (Sorghum bicolor L. Moench), a global staple food and forage crop, is among the most drought-adapted cereal crops, but its adaptation is not yet well understood. This study aims to better understand the genetic basis of preflowering drought in sorghum and identify loci underlying variation in water use and yield components under drought. A panel of 219 diverse sorghum from West Africa was phenotyped for yield components and water use in an outdoor large-tube lysimeter system under well-watered (WW) versus a preflowering drought water-stressed (WS) treatment. The experimental system was validated based on characteristic drought response in international drought tolerant check genotypes and genome-wide association studies (GWAS) that mapped the major height locus at QHT7.1 and Dw3. GWAS further identified marker trait associations (MTAs) for drought-related traits (plant height, flowering time, forage biomass, grain weight, water use) that each explained 7-70% of phenotypic variance. Most MTAs for drought-related traits correspond to loci not previously reported, but some MTA for forage biomass and grain weight under WS co-localized with staygreen post-flowering drought tolerance loci (Stg3a and Stg4). A globally common allele at S7_50055849 is associated with several yield components under drought, suggesting that it tags a major pleiotropic variant controlling assimilate partitioning to grain versus vegetative biomass. The GWAS revealed oligogenic variants for drought tolerance in sorghum landraces, which could be used as trait predictive markers for improved drought adaptation.
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Affiliation(s)
- Fanna Maina
- Department of AgronomyKansas State UniversityManhattanKansasUSA
- Institut National de la Recherche Agronomique du NigerNiameyNiger
| | - Abdou Harou
- International Crops Research Institute for the Semi‐Arid Tropics – Sahelian CenterNiameyNiger
| | - Falalou Hamidou
- International Crops Research Institute for the Semi‐Arid Tropics – Sahelian CenterNiameyNiger
- Department of Biology, Faculty of Sciences and TechnologyAbdou Moumouni UniversityNiameyNiger
| | - Geoffrey P. Morris
- Department of Soil & Crop ScienceColorado State UniversityFort CollinsColoradoUSA
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QTL mapping and genome-wide prediction of heat tolerance in multiple connected populations of temperate maize. Sci Rep 2019; 9:14418. [PMID: 31594984 PMCID: PMC6783442 DOI: 10.1038/s41598-019-50853-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 09/19/2019] [Indexed: 11/23/2022] Open
Abstract
Climate change will lead to increasing heat stress in the temperate regions of the world. The objectives of this study were the following: (I) to assess the phenotypic and genotypic diversity of traits related to heat tolerance of maize seedlings and dissect their genetic architecture by quantitative trait locus (QTL) mapping, (II) to compare the prediction ability of genome-wide prediction models using various numbers of KASP (Kompetitive Allele Specific PCR genotyping) single nucleotide polymorphisms (SNPs) and RAD (restriction site-associated DNA sequencing) SNPs, and (III) to examine the prediction ability of intra-, inter-, and mixed-pool calibrations. For the heat susceptibility index of five of the nine studied traits, we identified a total of six QTL, each explaining individually between 7 and 9% of the phenotypic variance. The prediction abilities observed for the genome-wide prediction models were high, especially for the within-population calibrations, and thus, the use of such approaches to select for heat tolerance at seedling stage is recommended. Furthermore, we have shown that for the traits examined in our study, populations created from inter-pool crosses are suitable training sets to predict populations derived from intra-pool crosses.
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High Morphological Differentiation in Crown Architecture Contrasts with Low Population Genetic Structure of German Norway Spruce Stands. FORESTS 2018. [DOI: 10.3390/f9120752] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
High elevation sites in the low mountain ranges in Germany are naturally covered by Norway spruce (Picea abies (Karst.) L.) stands. Historically, large scale anthropogenic range expansion starting in the mid to late 18th century had a huge impact on the forest composition throughout Germany. Utilisation and exploitation often led to artificial regeneration, mostly carried out using seeds from allochthonous provenances. Usually, autochthonous (natural) high elevation Norway spruce trees have narrow crown phenotypes, whereas lowland trees have broader crowns. Narrow crown phenotypes are likely the result of adaptation to heavy snow loads combined with high wind speeds. In the present study, neighbouring stand pairs of putative autochthonous and allochthonous origin with contrasting phenotypes in high elevation sites were investigated with 200 samples each. These stands are located in the Ore Mountains, the Thuringian Forest, and the Harz Mountains. Additionally, a relict population with the typical narrow high elevation phenotypes was sampled in Thuringia, known as “Schlossbergfichte”. The objective of the study was to quantify supposedly adaptive phenotypic differences in crown architecture and the genetic differentiation of 11 putatively neutral nuclear microsatellite markers (i.e., simple sequence repeats (nSSRs)). The high differentiation of morphological traits (PST = 0.952–0.989) between the neighbouring autochthonous and allochthonous stands of similar age contrasts with the very low neutral genetic differentiation (FST = 0.002–0.007; G″ST = 0.002–0.030), suggesting that directional selection at adaptive gene loci was involved in phenotypic differentiation. Comparing the regions, a small isolation by distance effect for the Harz Mountains was detected, suggesting landscape resistance restricting gene flow. Finally, the differentiation of the very old autochthonous (up to 250 years) stand “Schlossbergfichte” with typical high elevation phenotypes could cohere with the sampling of a relict genepool.
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David MC, Diaz FC, Mwanga ROM, Tumwegamire S, Mansilla RC, Grüneberg WJ. Gene Pool Subdivision of East African Sweetpotato Parental Material. CROP SCIENCE 2018; 58:2302-2314. [PMID: 33343014 PMCID: PMC7680937 DOI: 10.2135/cropsci2017.11.0695] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2017] [Accepted: 02/26/2018] [Indexed: 05/28/2023]
Abstract
Sweetpotato [Ipomoea batatas (L.) Lam] breeding is important for food security and health in East Africa (EA), and a breeding platform in Uganda provides national researchers and breeders in EA with true seed. Our objectives were to characterize genetic relationships among parental material used at the EA breeding platform. There were 135 parents and six check clones analyzed using 31 simple sequence repeat primers. An average of 7.13 alleles per primer was found, and Jaccard similarity coefficients were in the range of 0.298 to 1.00 with a mean of 0.542. Unweighted pair group cluster analysis placed most African parents in two main subclusters showing no association with morphology or geographical origin. The subclusters were also supported by principal coordinate analysis, derivative analysis of principal components, and population structure simulations. The analyzed breeding material from EA was highly genetically variable, grouped in two distinct genetic pools, and suitable to study heterosis exploiting breeding schemes.
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Affiliation(s)
- Maria C. David
- M.C. David, F.C. Diaz, and W.J. Grüneberg, International Potato Center (CIP), P.B. 1556 Lima 12, Peru
| | - Federico C. Diaz
- M.C. David, F.C. Diaz, and W.J. Grüneberg, International Potato Center (CIP), P.B. 1556 Lima 12, Peru
- R.O.M. Mwanga, CIP, P.B. 22274, Kampala, Uganda; S. Tumwegamire, International Institute of Tropical Agriculture (IITA), P.B. 34441, Dares-Salaam, Tanzania
- R.C. Mansilla, Univ. Nacional Agraria La Molina, P.B. 12-056, Lima 12, Peru
| | - Robert O. M. Mwanga
- R.O.M. Mwanga, CIP, P.B. 22274, Kampala, Uganda; S. Tumwegamire, International Institute of Tropical Agriculture (IITA), P.B. 34441, Dares-Salaam, Tanzania
| | - Silver Tumwegamire
- M.C. David, F.C. Diaz, and W.J. Grüneberg, International Potato Center (CIP), P.B. 1556 Lima 12, Peru
- R.O.M. Mwanga, CIP, P.B. 22274, Kampala, Uganda; S. Tumwegamire, International Institute of Tropical Agriculture (IITA), P.B. 34441, Dares-Salaam, Tanzania
- R.C. Mansilla, Univ. Nacional Agraria La Molina, P.B. 12-056, Lima 12, Peru
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Fiedler K, Bekele WA, Friedt W, Snowdon R, Stützel H, Zacharias A, Uptmoor R. Genetic dissection of the temperature dependent emergence processes in sorghum using a cumulative emergence model and stability parameters. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2012; 125:1647-1661. [PMID: 22847026 DOI: 10.1007/s00122-012-1941-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2012] [Accepted: 07/15/2012] [Indexed: 06/01/2023]
Abstract
Among the major limitations for cultivating biomass sorghum in temperate regions is low temperature in spring that results in low and non-uniform emergence. The adaptation of sorghum to tropical and subtropical highlands gives hint of genetic variation in cold tolerance during emergence. The objective of the present study was to detect marker-trait associations for parameters describing the emergence process under different temperature regimes. A diversity set comprising 194 genotypes was tested in nine controlled environments with temperatures ranging from 9.4 to 19.9 °C. The genotypes were fingerprinted with 171 DArT markers. A piecewise linear regression model carried out on cumulative emergence was used to estimate genotype mean performance across environments and to carry out stability analysis on the parameters of the regression model. Base temperature (T (b)) and thermal time required for emergence (E (TS)) were determined based on median time to emergence data. Identified QTL positions were compared to marker-trait associations for final emergence percentages under low (FEP(cold)) and normal (FEP(normal)) temperatures. QTL for mean final emergence percentage (FEP), FEP(cold) and FEP(normal,) T (b) and E (TS) were detected on SBI-01. Other QTL-rich regions were located on SBI-03, SBI-04, SBI-06, SBI-08, and SBI-09. Marker-trait associations for T (b) and E (TS) co-localized to QTL for the across environment stability of FEP and the median time to emergence or emergence rate, respectively. We conclude that genome regions on six chromosomes highly influencing cold tolerance during emergence are promising for regional association studies and for the development of stable markers for marker-assisted selection.
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Affiliation(s)
- Karin Fiedler
- Institute of Biological Production Systems, Leibniz Universität Hannover, Herrenhäuser Straße 2, 30419 Hannover, Germany.
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Bhosale SU, Stich B, Rattunde HFW, Weltzien E, Haussmann BIG, Hash CT, Ramu P, Cuevas HE, Paterson AH, Melchinger AE, Parzies HK. Association analysis of photoperiodic flowering time genes in west and central African sorghum [Sorghum bicolor (L.) Moench]. BMC PLANT BIOLOGY 2012; 12:32. [PMID: 22394582 PMCID: PMC3364917 DOI: 10.1186/1471-2229-12-32] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2011] [Accepted: 03/07/2012] [Indexed: 05/18/2023]
Abstract
BACKGROUND Photoperiod-sensitive flowering is a key adaptive trait for sorghum (Sorghum bicolor) in West and Central Africa. In this study we performed an association analysis to investigate the effect of polymorphisms within the genes putatively related to variation in flowering time on photoperiod-sensitive flowering in sorghum. For this purpose a genetically characterized panel of 219 sorghum accessions from West and Central Africa was evaluated for their photoperiod response index (PRI) based on two sowing dates under field conditions. RESULTS Sorghum accessions used in our study were genotyped for single nucleotide polymorphisms (SNPs) in six genes putatively involved in the photoperiodic control of flowering time. Applying a mixed model approach and previously-determined population structure parameters to these candidate genes, we found significant associations between several SNPs with PRI for the genes CRYPTOCHROME 1 (CRY1-b1) and GIGANTEA (GI). CONCLUSIONS The negative values of Tajima's D, found for the genes of our study, suggested that purifying selection has acted on genes involved in photoperiodic control of flowering time in sorghum. The SNP markers of our study that showed significant associations with PRI can be used to create functional markers to serve as important tools for marker-assisted selection of photoperiod-sensitive cultivars in sorghum.
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Affiliation(s)
- Sankalp U Bhosale
- Institute of Plant Breeding, Seed Science, and Population Genetics, University of Hohenheim, 70593 Stuttgart, Germany
| | - Benjamin Stich
- Max Planck Institute for Plant Breeding Research, 50829 Köln, Germany
| | - H Frederick W Rattunde
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) - Bamako, BP 320 Bamako, Mali
| | - Eva Weltzien
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) - Bamako, BP 320 Bamako, Mali
| | - Bettina IG Haussmann
- Institute of Plant Breeding, Seed Science, and Population Genetics, University of Hohenheim, 70593 Stuttgart, Germany
- ICRISAT - Sadoré, BP 12404 Niamey, Niger
| | - C Thomas Hash
- ICRISAT - Sadoré, BP 12404 Niamey, Niger
- ICRISAT - Patancheru, Hyderabad 502324, Andhra Pradesh, India
| | - Punna Ramu
- ICRISAT - Patancheru, Hyderabad 502324, Andhra Pradesh, India
| | - Hugo E Cuevas
- Plant Genome Mapping Laboratory, University of Georgia, Athens GA 30602, USA
- U.S. Dept. of Agriculture, Agricultural Research Service, Tropical Agriculture Research Station, 2200 P.A. Campos Ave., Mayaguez P.R. 00680, Puerto Rico
| | - Andrew H Paterson
- Plant Genome Mapping Laboratory, University of Georgia, Athens GA 30602, USA
| | - Albrecht E Melchinger
- Institute of Plant Breeding, Seed Science, and Population Genetics, University of Hohenheim, 70593 Stuttgart, Germany
| | - Heiko K Parzies
- Institute of Plant Breeding, Seed Science, and Population Genetics, University of Hohenheim, 70593 Stuttgart, Germany
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