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Daware A, Parida SK, Tyagi AK. Integrated Genomic Strategies for Cereal Genetic Enhancement: Combining QTL and Association Mapping. Methods Mol Biol 2020; 2072:15-25. [PMID: 31541435 DOI: 10.1007/978-1-4939-9865-4_3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Identification of genetic basis for important agronomic traits is essential for marker-assisted crop improvement. Linkage mapping is one of the most popular approaches utilized for identification of major quantitative trait loci (QTLs) governing important agronomic traits in cereals. However, the identified QTLs usually span large genomic intervals and very few of these are subsequently fine mapped to single major effect gene. This hinders application of these QTLs in marker-aided breeding and crop genetic enhancement. On the contrary, association mapping, another popular approach for identification of QTLs, provides very high resolution but suffers from high level of false positives. Joint linkage-association analysis provides a way to combine advantages and avoid the pitfalls associated with both these methods. In this context, we recently developed MetaQTL specific regional association analysis and demonstrated its utility to rapidly narrow down previously identified QTL intervals to few candidate genes. Here, we describe the detailed step-by-step guide for performing MetaQTL specific regional association analysis to identify important genomic regions and underlying potential major effect genes governing traits of agronomic importance in cereals.
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Almeida GD, Nair S, Borém A, Cairns J, Trachsel S, Ribaut JM, Bänziger M, Prasanna BM, Crossa J, Babu R. Molecular mapping across three populations reveals a QTL hotspot region on chromosome 3 for secondary traits associated with drought tolerance in tropical maize. Mol Breed 2014; 34:701-715. [PMID: 25076840 PMCID: PMC4092235 DOI: 10.1007/s11032-014-0068-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Accepted: 03/05/2014] [Indexed: 05/18/2023]
Abstract
Identifying quantitative trait loci (QTL) of sizeable effects that are expressed in diverse genetic backgrounds across contrasting water regimes particularly for secondary traits can significantly complement the conventional drought tolerance breeding efforts. We evaluated three tropical maize biparental populations under water-stressed and well-watered regimes for drought-related morpho-physiological traits, such as anthesis-silking interval (ASI), ears per plant (EPP), stay-green (SG) and plant-to-ear height ratio (PEH). In general, drought stress reduced the genetic variance of grain yield (GY), while that of morpho-physiological traits remained stable or even increased under drought conditions. We detected consistent genomic regions across different genetic backgrounds that could be target regions for marker-assisted introgression for drought tolerance in maize. A total of 203 QTL for ASI, EPP, SG and PEH were identified under both the water regimes. Meta-QTL analysis across the three populations identified six constitutive genomic regions with a minimum of two overlapping traits. Clusters of QTL were observed on chromosomes 1.06, 3.06, 4.09, 5.05, 7.03 and 10.04/06. Interestingly, a ~8-Mb region delimited in 3.06 harboured QTL for most of the morpho-physiological traits considered in the current study. This region contained two important candidate genes viz., zmm16 (MADS-domain transcription factor) and psbs1 (photosystem II unit) that are responsible for reproductive organ development and photosynthate accumulation, respectively. The genomic regions identified in this study partially explained the association of secondary traits with GY. Flanking single nucleotide polymorphism markers reported herein may be useful in marker-assisted introgression of drought tolerance in tropical maize.
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Affiliation(s)
- Gustavo Dias Almeida
- Universidade Federal de Viçosa (UFV), CEP: 36.570-000 Viçosa, Minas Gerais State Brazil
- Monsanto Company, CEP: 38.405-232 Uberlândia, Minas Gerais Brazil
| | - Sudha Nair
- International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, Mexico, DF Mexico
| | - Aluízio Borém
- Universidade Federal de Viçosa (UFV), CEP: 36.570-000 Viçosa, Minas Gerais State Brazil
| | - Jill Cairns
- International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, Mexico, DF Mexico
| | - Samuel Trachsel
- International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, Mexico, DF Mexico
| | - Jean-Marcel Ribaut
- Generation Challenge Program, Hosted by CIMMYT, Apdo. Postal 6-641, Mexico, DF Mexico
| | - Marianne Bänziger
- International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, Mexico, DF Mexico
| | | | - Jose Crossa
- International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, Mexico, DF Mexico
| | - Raman Babu
- International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, Mexico, DF Mexico
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