Genomic Selection in Plant Breeding: Methods, Models, and Perspectives

Crop yield reduction as a consequence of increasingly severe climatic events threatens global food security. Genetic loci that ensure productivity in challenging environments exist within the germplasm of crops, their wild relatives and species that are adapted to extreme environments. Selective breeding for the combination of beneficial loci in germplasm has improved yields in diverse environments throughout the history of agriculture. An effective new paradigm is the targeted identification of specific genetic determinants of stress adaptation that have evolved in nature and their precise introgression into elite varieties. These loci are often associated with distinct regulation or function, duplication and/or neofunctionalization of genes that maintain plant homeostasis.

Genetic mechanisms of abiotic stress tolerance that translate to crop yield stability.

Single nucleotide polymorphism (SNP) data can be obtained using one of the numerous uniplex or multiplex SNP genotyping platforms that combine a variety of chemistries, detection methods, and reaction formats. Kompetitive Allele Specific PCR (KASP) is one of the uniplex SNP genotyping platforms, and has evolved to be a global benchmark technology. However, there are no publications relating either to the technology itself or to its application in crop improvement programs. In this review, we provide an overview of the different aspects of the KASP genotyping platform, discuss its application in crop improvement, and compare it with the chip-based Illumina GoldenGate platform. The International Maize and Wheat Improvement Center routinely uses KASP, generating in excess of a million data points annually for crop improvement purposes. We found that (1) 81 % of the SNPs used in a custom-designed GoldenGate assay were transferable to KASP; (2) using KASP, negative controls (no template) consistently clustered together and rarely produced signals exceeding the threshold values for allele calling, in contrast to the situation observed using GoldenGate assays; (3) KASP’s average genotyping error in positive control DNA samples was 0.7–1.6 %, which is lower than that observed using GoldenGate (2.0–2.4 %); (4) KASP genotyping costs for marker-assisted recurrent selection were 7.9–46.1 % cheaper than those of the BeadXpress and GoldenGate platforms; and (5) KASP offers cost-effective and scalable flexibility in applications that require small to moderate numbers of markers, such as quality control analysis, quantitative trait loci (QTL) mapping in bi-parental populations, marker-assisted recurrent selection, marker-assisted backcrossing, and QTL fine mapping.

Single nucleotide polymorphism genotyping using Kompetitive Allele Specific PCR (KASP): overview of the technology and its application in crop improvement

Drought represents a major constraint on maize production worldwide. Understanding the genetic basis for natural variation in drought tolerance of maize may facilitate efforts to improve this trait in cultivated germplasm. Here, using a genome-wide association study, we show that a miniature inverted-repeat transposable element (MITE) inserted in the promoter of a NAC gene (ZmNAC111) is significantly associated with natural variation in maize drought tolerance. The 82-bp MITE represses ZmNAC111 expression via RNA-directed DNA methylation and H3K9 dimethylation when heterologously expressed in Arabidopsis. Increasing ZmNAC111 expression in transgenic maize enhances drought tolerance at the seedling stage, improves water-use efficiency and induces upregulation of drought-responsive genes under water stress. The MITE insertion in the ZmNAC111 promoter appears to have occurred after maize domestication and spread among temperate germplasm. The identification of this MITE insertion provides insight into the genetic basis for natural variation in maize drought tolerance.

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A transposable element in a NAC gene is associated with drought tolerance in maize seedlings

Maize production is threatened by drought stress worldwide. Identification of the genetic components underlying drought tolerance in maize is of great importance. Here we report a genome-wide association study (GWAS) of maize drought tolerance at the seedling stage that identified 83 genetic variants, which were resolved to 42 candidate genes. The peak GWAS signal showed that the natural variation in ZmVPP1, encoding a vacuolar-type H(+) pyrophosphatase, contributes most significantly to the trait. Further analysis showed that a 366-bp insertion in the promoter, containing three MYB cis elements, confers drought-inducible expression of ZmVPP1 in drought-tolerant genotypes. Transgenic maize with enhanced ZmVPP1 expression exhibits improved drought tolerance that is most likely due to enhanced photosynthetic efficiency and root development. Taken together, this information provides important genetic insights into the natural variation of maize drought tolerance. The identified loci or genes can serve as direct targets for both genetic engineering and selection for maize trait improvement.

Genetic variation in ZmVPP1 contributes to drought tolerance in maize seedlings

Genomic selection incorporates all the available marker information into a model to predict genetic values of breeding progenies for selection. The objective of this study was to estimate genetic gains in grain yield from genomic selection (GS) in eight bi-parental maize populations under managed drought stress environments. In each population, 148 to 300 F₂:₃ (C₀) progenies were derived and crossed to a single-cross tester from a complementary heterotic group. The resulting testcrosses of each population were evaluated under two to four managed drought stress and three to four well-watered conditions in different locations and genotyped with 191 to 286 single nucleotide polymorphism (SNP) markers. The top 10% families were selected from C₀ using a phenotypic selection index and were intermated to form C₁. Selections both at C₁ and C₂ were based on genomic estimated breeding values (GEBVs). The best lines from C₀ were also advanced using a pedigree selection scheme. For genetic gain studies, a total of 55 entries representing the eight populations were crossed to a single-cross tester, and evaluated in four managed drought stress environments. Each population was represented by bulk seed containing equal amounts of seed of C₀, C₁, C₂, C₃, parents, F₁s, and lines developed via pedigree selection. Five commercial checks were included for comparison. The average gain from genomic selection per cycle across eight populations was 0.086 Mg ha–¹. The average grain yield of C₃–derived hybrids was significantly higher than that of hybrids derived from C₀. Hybrids derived from C₃ produced 7.3% (0.176 Mg ha–¹) higher grain yield than those developed through the conventional pedigree breeding method. The study demonstrated that genomic selection is more effective than pedigree-based conventional phenotypic selection for increasing genetic gains in grain yield under drought stress in tropical maize.

https://acsess.onlinelibrary.wiley.com/doi/pdf/10.2135/cropsci2014.07.0460

Genetic Gains in Grain Yield Through Genomic Selection in Eight Bi-parental Maize Populations under Drought Stress

Identification of QTL with large phenotypic effects conserved across genetic backgrounds and environments is one of the prerequisites for crop improvement using marker assisted selection (MAS). The objectives of this study were to identify meta-QTL (mQTL) for grain yield (GY) and anthesis silking interval (ASI) across 18 bi-parental maize populations evaluated in the same conditions across 2-4 managed water stressed and 3-4 well watered environments. The meta-analyses identified 68 mQTL (9 QTL specific to ASI, 15 specific to GY, and 44 for both GY and ASI). Mean phenotypic variance explained by each mQTL varied from 1.2 to 13.1% and the overall average was 6.5%. Few QTL were detected under both environmental treatments and/or multiple (>4 populations) genetic backgrounds. The number and 95% genetic and physical confidence intervals of the mQTL were highly reduced compared to the QTL identified in the original studies. Each physical interval of the mQTL consisted of 5 to 926 candidate genes. Meta-analyses reduced the number of QTL by 68% and narrowed the confidence intervals up to 12-fold. At least the 4 mQTL (mQTL2.2, mQTL6.1, mQTL7.5 and mQTL9.2) associated with GY under both water-stressed and well-watered environments and detected up to 6 populations may be considered for fine mapping and validation to confirm effects in different genetic backgrounds and pyramid them into new drought resistant breeding lines. This is the first extensive report on meta-analysis of data from over 3100 individuals genotyped using the same SNP platform and evaluated in the same conditions across a wide range of managed water-stressed and well-watered environments.

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Meta-analyses of QTL for grain yield and anthesis silking interval in 18 maize populations evaluated under water-stressed and well-watered environments

In marker-assisted recurrent selection (MARS), a subset of molecular markers significantly associated with target traits of interest are used to predict the breeding value of individual plants, followed by rapid recombination and selfing. This study estimated genetic gains in grain yield (GY) using MARS in 10 biparental tropical maize (Zea may L.) populations. In each population, 148 to 184 F2:3 (defined as C0) progenies were derived, crossed with a single-cross tester, and evaluated under water-stressed (WS) and well-watered (WW) environments in subSaharan Africa (SSA). The C0 populations were genotyped with 190 to 225 single-nucleotide polymorphism (SNP) markers. A selection index based on marker data and phenotypic data was used for selecting the best C0 families for recombination. Individual plants from selected families were genotyped using 55 to 87 SNPs tagging specific quantitative trait loci (QTL), and the best individuals from each cycle were either intercrossed (to form C1) or selfed (to form C1S1 and C1S2). A genetic gain study was conducted using test crosses of lines from the different cycles F1 and founder parents. Test crosses, along with five commercial hybrid checks were evaluated under four WS and four WW environments. The overall gain for GY using MARS across the 10 populations was 105 kg ha−1 yr−1 under WW and 51 kg ha−1 yr−1 under WS. Across WW environments, GY of C1S2–derived hybrids were 8.7, 5.9, and 16.2% significantly greater than those of C0, founder parents, and commercial checks, respectively. Results demonstrate the potential of MARS for increasing genetic gain under both drought and optimum environments in SSA. Y. Beyene, K. Semagn, S. Mugo, L. Machida, M. Olsen, and B.M. Prasanna, International Maize and Wheat Improvement Center (CIMMYT), P. O. Box 1041, Village Market 00621, Nairobi, Kenya; J. Crossa, G. Alvarado, M. Bänziger; CIMMYT, Apdo. Postal 6-641, 06600, Mexico DF, Mexico; G.N. Atlin, Bill and Melinda Gates Foundation, Seattle, WA, USA; A. Tarekegne, CIMMYT, 12.5 Km peg Mazowe Road, P.O. Box MP163, Mount Pleasant, Harare, Zimbabwe; B. Meisel, Monsanto South Africa (Pty) Ltd, P. O. Box 69933, Bryanston, 2021, South Africa; P. Sehabiague, Monsanto SAS, Croix de Pardies, BP21, 40305 Peyrehorade, France; B.S. Vivek, CIMMYTIndia, c/o ICRISAT, Patancheru 502324, India; S. Oikeh, African Agricultural Technology Foundation (AATF), P.O. Box 30709-00100, Nairobi, Kenya. Received 28 Feb. 2015. Accepted 26 Aug. 2015. *Corre sponding author (y.beyene@cgiar.org). Abbreviations: AD, anthesis date; ASI, anthesis–silking interval; GS, genomic selection; GY, grain yield; MABC, marker-assisted backcrossing; MARS, marker-assisted recurrent selection; MAS, marker-assisted selection; mQTL, meta-QTL; P-MTI, multiple-trait phenotypic index; PH, plant height; QC, quality control; QTL, quantitative trait loci; SD, silking date; SNP, single-nucleotide polymorphism; SSA, sub-Saharan Africa; WS, water-stressed; WW, well-watered. Published in Crop Sci. 56:344–353 (2016). doi: 10.2135/cropsci2015.02.0135 Freely available online through the author-supported open-access option. © Crop Science Society of America | 5585 Guilford Rd., Madison, WI 53711 USA All rights reserved. Published November 23, 2015

Improving Maize Grain Yield under Drought Stress and Non-stress Environments in Sub-Saharan Africa using Marker-Assisted Recurrent Selection

A marker-assisted recurrent selection (MARS) program was undertaken in sub-Saharan Africa to improve grain yield under drought-stress in 10 biparental tropical maize populations. The objectives of the present study were to evaluate the performance of C1S2-derived hybrids obtained after three MARS cycles (one cycle of recombination (C1), followed by two generations of selfing (S2), and to study yield stability under both drought-stress (DS) and well-watered (WW) conditions. For each of the 10 populations, we evaluated hybrids developed by crossing 47–74 C1S2 lines advanced through MARS, the best five S5 lines developed through pedigree selection, and the founder parents with a single-cross tester from a complementary heterotic group. The hybrids and five commercial checks were evaluated in Kenya under 1–3 DS and 3–5 WW conditions with two replications. Combined across DS locations, the top 10 C1S2-derived hybrids from each of the 10 biparental populations produced 0.5–46.3 and 11.1–55.1 % higher mean grain yields than hybrids developed using pedigree selection and the commercial checks, respectively. Across WW locations, the best 10 hybrids derived from C1S2 of each population produced 3.4–13.3 and 7.9–36.5 % higher grain yields than hybrids derived using conventional pedigree breeding and the commercial checks, respectively. Mean days to anthesis of the best 10 C1S2 hybrids were comparable to those of hybrids developed using the pedigree method, the founder parents and the commercial checks, with a maximum difference of 3.5 days among the different groups. However, plant height was significantly (P < 0.01) different in most pairwise comparisons. Our results showed the superiority of MARS over pedigree selection for improving diverse tropical maize populations as sources of improved lines for stress-prone environments and thus MARS can be effectively integrated into mainstream maize breeding programs.

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Pierre Sehabiague

Papers

Genetic Gains in Grain Yield Through Genomic Selection in Eight Bi-parental Maize Populations under Drought Stress

Meta-analyses of QTL for grain yield and anthesis silking interval in 18 maize populations evaluated under water-stressed and well-watered environments

Improving Maize Grain Yield under Drought Stress and Non-stress Environments in Sub-Saharan Africa using Marker-Assisted Recurrent Selection

Performance and grain yield stability of maize populations developed using marker-assisted recurrent selection and pedigree selection procedures