1
|
Carlson CH, Fiedler JD, Naraghi SM, Nazareno ES, Ardayfio NK, McMullen MS, Kianian SF. Archetypes of inflorescence: genome-wide association networks of panicle morphometric, growth, and disease variables in a multiparent oat population. Genetics 2022; 223:6700642. [PMID: 36106985 PMCID: PMC9910404 DOI: 10.1093/genetics/iyac128] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 08/18/2022] [Indexed: 11/13/2022] Open
Abstract
There is limited information regarding the morphometric relationships of panicle traits in oat (Avena sativa) and their contribution to phenology and growth, physiology, and pathology traits important for yield. To model panicle growth and development and identify genomic regions associated with corresponding traits, 10 diverse spring oat mapping populations (n = 2,993) were evaluated in the field and 9 genotyped via genotyping-by-sequencing. Representative panicles from all progeny individuals, parents, and check lines were scanned, and images were analyzed using manual and automated techniques, resulting in over 60 unique panicle, rachis, and spikelet variables. Spatial modeling and days to heading were used to account for environmental and phenological variances, respectively. Panicle variables were intercorrelated, providing reproducible archetypal and growth models. Notably, adult plant resistance for oat crown rust was most prominent for taller, stiff stalked plants having a more open panicle structure. Within and among family variance for panicle traits reflected the moderate-to-high heritability and mutual genome-wide associations (hotspots) with numerous high-effect loci. Candidate genes and potential breeding applications are discussed. This work adds to the growing genetic resources for oat and provides a unique perspective on the genetic basis of panicle architecture in cereal crops.
Collapse
Affiliation(s)
- Craig H Carlson
- Corresponding author: Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, USDA-ARS, Fargo, ND, 58102, USA.
| | - Jason D Fiedler
- Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, USDA-ARS, Fargo, ND 58102, USA
| | | | - Eric S Nazareno
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108, USA
| | - Naa Korkoi Ardayfio
- Department of Plant Sciences, North Dakota State University, Fargo, ND 58105, USA
| | - Michael S McMullen
- Department of Plant Sciences, North Dakota State University, Fargo, ND 58105, USA
| | | |
Collapse
|
2
|
Rabbi SMHA, Kumar A, Mohajeri Naraghi S, Simsek S, Sapkota S, Solanki S, Alamri MS, Elias EM, Kianian S, Missaoui A, Mergoum M. Genome-Wide Association Mapping for Yield and Related Traits Under Drought Stressed and Non-stressed Environments in Wheat. Front Genet 2021; 12:649988. [PMID: 34239537 PMCID: PMC8258415 DOI: 10.3389/fgene.2021.649988] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 04/28/2021] [Indexed: 12/02/2022] Open
Abstract
Understanding the genetics of drought tolerance in hard red spring wheat (HRSW) in northern USA is a prerequisite for developing drought-tolerant cultivars for this region. An association mapping (AM) study for drought tolerance in spring wheat in northern USA was undertaken using 361 wheat genotypes and Infinium 90K single-nucleotide polymorphism (SNP) assay. The genotypes were evaluated in nine different locations of North Dakota (ND) for plant height (PH), days to heading (DH), yield (YLD), test weight (TW), and thousand kernel weight (TKW) under rain-fed conditions. Rainfall data and soil type of the locations were used to assess drought conditions. A mixed linear model (MLM), which accounts for population structure and kinship (PC+K), was used for marker–trait association. A total of 69 consistent QTL involved with drought tolerance-related traits were identified, with p ≤ 0.001. Chromosomes 1A, 3A, 3B, 4B, 4D, 5B, 6A, and 6B were identified to harbor major QTL for drought tolerance. Six potential novel QTL were identified on chromosomes 3D, 4A, 5B, 7A, and 7B. The novel QTL were identified for DH, PH, and TKW. The findings of this study can be used in marker-assisted selection (MAS) for drought-tolerance breeding in spring wheat.
Collapse
Affiliation(s)
- S M Hisam A Rabbi
- Department of Plant Sciences, North Dakota State University, Fargo, ND, United States
| | - Ajay Kumar
- Department of Plant Sciences, North Dakota State University, Fargo, ND, United States
| | | | - Senay Simsek
- Department of Plant Sciences, North Dakota State University, Fargo, ND, United States
| | - Suraj Sapkota
- Institute of Plant Breeding, Genetics, and Genomics, University of Georgia, Griffin, GA, United States
| | - Shyam Solanki
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, United States
| | - Mohammed S Alamri
- Department of Food Sciences and Nutrition, King Saud University, Riyadh, Saudi Arabia
| | - Elias M Elias
- Department of Plant Sciences, North Dakota State University, Fargo, ND, United States
| | - Shahryar Kianian
- United States Department of Agriculture-The Agricultural Research Service (USDA-ARS) Cereal Disease Laboratory, University of Minnesota, St. Paul, MN, United States
| | - Ali Missaoui
- Institute of Plant Breeding, Genetics, and Genomics, University of Georgia, Griffin, GA, United States.,Department of Crop and Soil Sciences, University of Georgia, Griffin, GA, United States
| | - Mohamed Mergoum
- Institute of Plant Breeding, Genetics, and Genomics, University of Georgia, Griffin, GA, United States.,Department of Crop and Soil Sciences, University of Georgia, Griffin, GA, United States
| |
Collapse
|
3
|
Rabbi SMHA, Kumar A, Mohajeri Naraghi S, Sapkota S, Alamri MS, Elias EM, Kianian S, Seetan R, Missaoui A, Solanki S, Mergoum M. Identification of Main-Effect and Environmental Interaction QTL and Their Candidate Genes for Drought Tolerance in a Wheat RIL Population Between Two Elite Spring Cultivars. Front Genet 2021; 12:656037. [PMID: 34220939 PMCID: PMC8249774 DOI: 10.3389/fgene.2021.656037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 05/13/2021] [Indexed: 01/22/2023] Open
Abstract
Understanding the genetics of drought tolerance can expedite the development of drought-tolerant cultivars in wheat. In this study, we dissected the genetics of drought tolerance in spring wheat using a recombinant inbred line (RIL) population derived from a cross between a drought-tolerant cultivar, ‘Reeder’ (PI613586), and a high-yielding but drought-susceptible cultivar, ‘Albany.’ The RIL population was evaluated for grain yield (YLD), grain volume weight (GVW), thousand kernel weight (TKW), plant height (PH), and days to heading (DH) at nine different environments. The Infinium 90 k-based high-density genetic map was generated using 10,657 polymorphic SNP markers representing 2,057 unique loci. Quantitative trait loci (QTL) analysis detected a total of 11 consistent QTL for drought tolerance-related traits. Of these, six QTL were exclusively identified in drought-prone environments, and five were constitutive QTL (identified under both drought and normal conditions). One major QTL on chromosome 7B was identified exclusively under drought environments and explained 13.6% of the phenotypic variation (PV) for YLD. Two other major QTL were detected, one each on chromosomes 7B and 2B under drought-prone environments, and explained 14.86 and 13.94% of phenotypic variation for GVW and YLD, respectively. One novel QTL for drought tolerance was identified on chromosome 2D. In silico expression analysis of candidate genes underlaying the exclusive QTLs associated with drought stress identified the enrichment of ribosomal and chloroplast photosynthesis-associated proteins showing the most expression variability, thus possibly contributing to stress response by modulating the glycosyltransferase (TraesCS6A01G116400) and hexosyltransferase (TraesCS7B01G013300) unique genes present in QTL 21 and 24, respectively. While both parents contributed favorable alleles to these QTL, unexpectedly, the high-yielding and less drought-tolerant parent contributed desirable alleles for drought tolerance at four out of six loci. Regardless of the origin, all QTL with significant drought tolerance could assist significantly in the development of drought-tolerant wheat cultivars, using genomics-assisted breeding approaches.
Collapse
Affiliation(s)
- S M Hisam Al Rabbi
- Department of Plant Sciences, North Dakota State University, Fargo, ND, United States
| | - Ajay Kumar
- Department of Plant Sciences, North Dakota State University, Fargo, ND, United States
| | | | - Suraj Sapkota
- Institute of Plant Breeding, Genetics, and Genomics, University of Georgia, Griffin, GA, United States
| | - Mohammed S Alamri
- Department of Food Science and Nutrition, King Saud University, Riyadh, Saudi Arabia
| | - Elias M Elias
- Department of Plant Sciences, North Dakota State University, Fargo, ND, United States
| | - Shahryar Kianian
- USDA-ARS Cereal Disease Laboratory, University of Minnesota, St. Paul, MN, United States
| | - Raed Seetan
- Department of Computer Science, Slippery Rock University, Slippery Rock, PA, United States
| | - Ali Missaoui
- Institute of Plant Breeding, Genetics, and Genomics, University of Georgia, Griffin, GA, United States.,Department of Crop and Soil Sciences, University of Georgia, Griffin, GA, United States
| | - Shyam Solanki
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, United States
| | - Mohamed Mergoum
- Institute of Plant Breeding, Genetics, and Genomics, University of Georgia, Griffin, GA, United States.,Department of Crop and Soil Sciences, University of Georgia, Griffin, GA, United States
| |
Collapse
|
4
|
Mohajeri Naraghi S, Mardi M, Hasanloo T, Pirseyedi SM, Mahmoodi P. Isolation and characterization of novel microsatellite loci in Vaccinium arctostaphylos L. CONSERV GENET RESOUR 2011. [DOI: 10.1007/s12686-010-9375-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|