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Agriculture
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Feature Papers in Genotype Evaluation and Breeding
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Feature Papers in Genotype Evaluation and Breeding

A special issue of Agriculture (ISSN 2077-0472). This special issue belongs to the section "Crop Genetics, Genomics and Breeding".

Deadline for manuscript submissions: closed (5 September 2024) | Viewed by 16436

Special Issue Editor

Prof. Dr. Rodomiro Ortiz

E-Mail Website
Guest Editor
Department of Plant Breeding, Swedish University of Agricultural Sciences, SE 2 3053 Alnarp, Sweden
Interests: agrobiodiversity; food security; genetic resources; genetics; plant breeding
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

“The secret of improved plant breeding, apart

from scientific knowledge,

is love”

Luther Burbank

Dear Colleagues,

Plant breeding aims to provide improved cultivars that address human needs. These cultivars must show enhanced productivity, appropriate produce quality (for food, feed, fiber, fuel, feedstock, flower, fun and pharmaceuticals), climate resilience, and host plant resistance to pathogens and pests. Plant breeding contributes further to sustainable agriculture intensification by reducing the negative impacts on agroecosystems by releasing cultivars with input use efficiency (“producing more or the same with less”) and that are suitable for conservation agriculture. This Special Issue on “Feature Papers in Genotype Evaluation and Breeding” will thus focus on the scientific and technical advances in knowledge, methods and tools that facilitate and accelerate the release of genetically enhanced seed-embedded technology that meets the current and future expectations of markets worldwide. Research or review articles on the following topics are welcome for this Special Issue:

  • How to improve selection accuracy considering the product profiles?
  • What may work for increasing genetic gains and steady cultivar replacement?
  • Where to breed crops for the future?
  • When to increase genetic variation in the breeding pool?
  • Which breeding methods and tools may enhance selection intensity?
  • Who will deliver the seeds of cultivars in 2050?

Prof. Dr. Rodomiro Ortiz
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Agriculture is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • cultivar testing
  • enviromics
  • germplasm enhancement
  • genetic gains
  • genomics
  • genotype–environment interaction
  • phenomics
  • pre-breeding
  • participatory variety selection
  • population improvement

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Published Papers (9 papers)

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Research

Jump to: Review

16 pages, 3201 KiB  
Article
Integrating Environmental Covariates into Adaptability and Stability Analyses: A Structural Equation Modeling Approach for Cotton Breeding
by Matheus Massariol Suela, Moysés Nascimento, Ana Carolina Campana Nascimento, Camila Ferreira Azevedo, Paulo Eduardo Teodoro, Francisco José Correia Farias, Luiz Paulo de Carvalho and Diego Jarquin
Agriculture 2024, 14(11), 1914; https://doi.org/10.3390/agriculture14111914 - 28 Oct 2024
Viewed by 847
Abstract
Breeding programs rely on genotype-by-environment interaction (GEI) to recommend cultivars for specific locations. GEI describes how different genotypes perform under varying environmental conditions. Several methods were proposed to assess adaptability and stability across environments. These methods utilize various statistical approaches like parametric and [...] Read more.
Breeding programs rely on genotype-by-environment interaction (GEI) to recommend cultivars for specific locations. GEI describes how different genotypes perform under varying environmental conditions. Several methods were proposed to assess adaptability and stability across environments. These methods utilize various statistical approaches like parametric and non-parametric regression, multivariate analysis techniques, and even Bayesian frameworks and artificial intelligence. The accessibility of environmental data through platforms like NASA POWER allows breeders to integrate this information into a breeding process. It has been done by using multi-omics integration models that combine data across various biological levels to create accurate predictive models. In the context of phenotypic adaptability and stability analysis, structural equation modeling (SEM) offers an interesting approach to integrating environmental covariates. This work aimed to propose a novel approach that integrates weather information into adaptability and stability analysis, combining SEM with the established Eberhart and Russell model. Additionally, a user-friendly applet, denoted ECERSEM-AdaptStab, was made available to perform the analysis. This approach utilized data from 12 cotton cultivar trials conducted across two growing seasons at 19 sites. This approach successfully integrated environmental covariates into a phenotypic adaptability and stability analysis of cotton cultivars. Specifically, the genotypes TMG 41 WS, IMA CV 690, DP 555 BGRR, BRS 286 and BRS 369 RF were recommended for favorable environments, while the genotypes TMG 43 WS, IMA 5675 B2RF, IMA 08 WS, NUOPAL, DELTA OPAL, BRS 335, and BRS 368 RF are more suitable for unfavorable environments. Full article
(This article belongs to the Special Issue Feature Papers in Genotype Evaluation and Breeding)
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21 pages, 7061 KiB  
Article
Screening New Mungbean Varieties for Terminal Drought Tolerance
by Sobia Ikram, Surya Bhattarai and Kerry B. Walsh
Agriculture 2024, 14(8), 1328; https://doi.org/10.3390/agriculture14081328 - 9 Aug 2024
Cited by 1 | Viewed by 795
Abstract
Rainfed mungbean crops in Queensland Australia frequently experience terminal drought (drought stress in the final stages of reproductive development), highlighting the importance of drought-tolerant varieties for sustainable mungbean production. Given there is limited information on the relative drought tolerance of current mungbean varieties [...] Read more.
Rainfed mungbean crops in Queensland Australia frequently experience terminal drought (drought stress in the final stages of reproductive development), highlighting the importance of drought-tolerant varieties for sustainable mungbean production. Given there is limited information on the relative drought tolerance of current mungbean varieties in Australia, the study of genetic variations and mechanisms of drought tolerance in summer mungbean can provide a basis for developing drought-tolerant mungbean varieties. This study evaluated the physiological, biochemical, and phenological traits underpinning yield attributes associated with drought tolerance in selected mungbean varieties. Four new mungbean varieties (AVTMB#1 to 4) and the Australian commercial line (Jade-AU) were grown in tall (75 cm) polyvinyl chloride (PVC) lysimeters where drought stress was imposed at the early flowering stage (R1) and maintained until maturity. Drought stress significantly impacted all the varieties. Averaged across all the varieties, drought stress was associated with a reduction in stomatal conductance (gs) and photosynthetic rate (Asat) by 78% and 86%, respectively, compared to well-watered plants. Internal carbon dioxide concentration (Ci), the effective quantum yield of photosystem II (ΦPSII) and maximum light-use efficiency of light-acclimated photosystem II (PSII) centres (Fv’/Fm’) were also decreased, while excitation pressure (1-qP) increased with drought treatment. A positive correlation (r = 0.60) existed between seed yield and ΦPSII assessed at R1, while a weak correlation with Fv’/Fm’ (r = 0.24) was observed. Excitation pressure (1-qP) at the R1 stage was negatively correlated with seed yield (r = −0.66). Therefore, leaf fluorescence measures, viz., 1-qP and ΦPSII, were recommended for use in screening mungbean varieties for drought tolerance. The varieties, AVTMB#1 and AVTMB#4, respectively achieved 39 and 38% greater seed yields relative to the commercial variety, Jade-AU, under terminal drought conditions. Full article
(This article belongs to the Special Issue Feature Papers in Genotype Evaluation and Breeding)
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13 pages, 2982 KiB  
Article
Oil Quality Prediction in Olive Oil by Near-Infrared Spectroscopy: Applications in Olive Breeding
by Hande Yılmaz-Düzyaman, Raúl de la Rosa, Leonardo Velasco, Nieves Núñez-Sánchez and Lorenzo León
Agriculture 2024, 14(5), 721; https://doi.org/10.3390/agriculture14050721 - 2 May 2024
Viewed by 2106
Abstract
The oxidative stability index (OSI) and fatty acid (FA) composition of extra virgin olive oils (EVOOs) are key parameters in the characterization of new varieties in breeding programs. Their determination through traditional methods (Rancimat and gas chromatography, respectively) is expensive and time-consuming. Therefore, [...] Read more.
The oxidative stability index (OSI) and fatty acid (FA) composition of extra virgin olive oils (EVOOs) are key parameters in the characterization of new varieties in breeding programs. Their determination through traditional methods (Rancimat and gas chromatography, respectively) is expensive and time-consuming. Therefore, there is a need to develop rapid and cost-effective analytical procedures. This study aimed to evaluate the potential use of near-infrared spectroscopy (NIRS) for analyzing OSI and FA composition in EVOOs. A total of 318 samples sourced from different origins were evaluated using both FT-NIR MPA and MicroNIR instruments in transmittance mode, with wavelengths ranging from 1100 to 2500 nm and 908 to 1676 nm, respectively. Different accuracies were obtained in the models developed for the different evaluated traits, with simpler models (using a lower number of latent variables) for the MPA analyzer in all cases. Additionally, consistent results between instruments for the partitioning of the variance and heritability estimation, and the reliable ranking of genotypes were obtained from one of the sample sets tested. In summary, models derived from PLS regression using spectroscopic data of both instruments demonstrated promising results in determining these EVOO traits, facilitating their evaluation and selection of genotypes, particularly in breeding programs. Full article
(This article belongs to the Special Issue Feature Papers in Genotype Evaluation and Breeding)
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20 pages, 8175 KiB  
Article
Genetic Enhancement of Blast and Bacterial Leaf Blight Resistance in Rice Variety CO 51 through Marker-Assisted Selection
by Samuthirapandi Subburaj, Thiyagarajan Thulasinathan, Viswabharathy Sakthivel, Bharathi Ayyenar, Rohit Kambale, Veera Ranjani Rajagopalan, Sudha Manickam, Raghu Rajasekaran, Gopalakrishnan Chellappan, Kalaimagal Thiyagarajan, Manonmani Swaminathan and Raveendran Muthurajan
Agriculture 2024, 14(5), 693; https://doi.org/10.3390/agriculture14050693 - 28 Apr 2024
Cited by 1 | Viewed by 1439
Abstract
The increased use of chemicals in rice farming poses significant issues regarding the emergence of pesticide/fungicide resistance and environmental sustainability concerns. This study was aimed at the genetic improvement of blast, bacterial leaf blight (BB) and gall midge resistance in a popular rice [...] Read more.
The increased use of chemicals in rice farming poses significant issues regarding the emergence of pesticide/fungicide resistance and environmental sustainability concerns. This study was aimed at the genetic improvement of blast, bacterial leaf blight (BB) and gall midge resistance in a popular rice variety CO 51 which already harbours a blast resistance gene Pi54. Efforts were made to pyramid an additional blast resistance gene Pi9 along with two BB resistance genes (xa13 and Xa21) and two gall midge resistance genes (Gm1 and Gm4) into an elite rice variety CO 51 to enhance the resistance level to biotic stresses. The superior lines were selected using functional markers conferring resistance to blast (NBS4 and Pi54MAS linked to Pi9 and Pi54 genes, respectively) and BB [(xa13Prom (xa13) and pTA248 (Xa21)] and SSR markers linked to Gm1 (RM1328) and Gm4 (RM22550) for phenotypic screening and agronomic evaluation. The genotyping and phenotyping of F6 and BC2F6 progenies of CO 51 X 562-4, for agronomic traits and resistance to BB and blast, identified ten superior progenies in F6 and five superior progenies in BC2F6. The breeding lines harbouring both xa13+Xa21 exhibited high levels of resistance to BB (score ≤ 1 cm) and Pi9+Pi54 exhibited strong resistance to blast (score ≤ 2). Identified lines can be evaluated further for varietal improvement or utilised as genetic stocks in breeding programs. Full article
(This article belongs to the Special Issue Feature Papers in Genotype Evaluation and Breeding)
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12 pages, 619 KiB  
Article
Genomic Prediction for Inbred and Hybrid Polysomic Tetraploid Potato Offspring
by Rodomiro Ortiz, Fredrik Reslow, Ramesh Vetukuri, M. Rosario García-Gil, Paulino Pérez-Rodríguez and José Crossa
Agriculture 2024, 14(3), 455; https://doi.org/10.3390/agriculture14030455 - 11 Mar 2024
Viewed by 4045
Abstract
Potato genetic improvement begins with crossing cultivars or breeding clones which often have complementary characteristics for producing heritable variation in segregating offspring, in which phenotypic selection is used thereafter across various vegetative generations (Ti). The aim of this research was to [...] Read more.
Potato genetic improvement begins with crossing cultivars or breeding clones which often have complementary characteristics for producing heritable variation in segregating offspring, in which phenotypic selection is used thereafter across various vegetative generations (Ti). The aim of this research was to determine whether tetrasomic genomic best linear unbiased predictors (GBLUPs) may facilitate selecting for tuber yield across early Ti within and across breeding sites in inbred (S1) and hybrid (F1) tetraploid potato offspring. This research used 858 breeding clones for a T1 trial at Umeå (Norrland, 63°49′30″ N 20°15′50″ E) in 2021, as well as 829 and 671 clones from the breeding population for T2 trials during 2022 at Umeå and Helgegården (Skåne, 56°01′46″ N 14°09′24″ E), respectively, along with their parents (S0) and check cultivars. The S1 and F1 were derived from selfing and crossing four S0. The experimental layout was an augmented design of four-plant plots across testing sites, where breeding clones were non-replicated, and the parents and cultivars were placed in all blocks between the former. The genomic prediction abilities (r) for tuber weight per plant were 0.5944 and 0.6776 in T2 at Helgegården and Umeå, respectively, when T1 at Umeå was used as the training population. On average, r was larger in inbred than in hybrid offspring at both breeding sites. The r was also estimated using multi-environment data (involving at least one S1 and one F1) for T2 performance at both breeding sites. The r was strongly influenced by the genotype in both S1 and F1 offspring irrespective of the breeding site. Full article
(This article belongs to the Special Issue Feature Papers in Genotype Evaluation and Breeding)
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14 pages, 4130 KiB  
Article
Genetic Improvement of Drought Tolerance in a Mega-Rice Variety Improved White Ponni through Marker-Assisted Backcross Breeding
by F. D. Prisca Seeli, Muthukumar Manoharan, Bharathi Ayyenar, Rohit Kambale, Vignesh Mohanavel, Veera Ranjani Rajagopalan, Sudha Manickam, Raveendran Muthurajan and Manonmani Swaminathan
Agriculture 2024, 14(3), 431; https://doi.org/10.3390/agriculture14030431 - 7 Mar 2024
Viewed by 1738
Abstract
In the ever-changing climatic conditions, it has become important to enhance rice productivity to ensure global food security. Drought is one of the major limiting factors in rice pro- duction. Drought during the reproductive stage results in maximum or complete yield loss. Efforts [...] Read more.
In the ever-changing climatic conditions, it has become important to enhance rice productivity to ensure global food security. Drought is one of the major limiting factors in rice pro- duction. Drought during the reproductive stage results in maximum or complete yield loss. Efforts have been taken to develop drought-tolerant rice lines by introgressing three major drought-effect QTLs, viz. qDTY1.1, qDTY2.1, and qDTY3.1, from Apo into a susceptible popular rice variety, Improved White Ponni (IWP). Backcross inbred lines of IWP × Apo were developed through the marker-assisted backcross breeding approach. Foreground analysis using linked markers resulted in the identification of 17 progenies carrying two or more QTLs, and the recurrent parent genome recoveries of these lines were >95.6% using 72 genome-wide SSR markers distributed throughout all chromosomes. Upon phenotypic evaluation of 17 IWP BILs, the water limited condition resulted in the identification of improved lines by recording the yield and the yield-related parameters. The promising performance of IWP BILs in terms of spikelet fertility (63.3%) and grain yield per plant (>10 g) under drought stress indicated the positive effects of introgressed qDTYs, while IWP recorded complete yield loss (94.2%). Out of the cultivars considered, the best-performing lines which truly exhibited drought tolerance, with more increased yield than the recurrent parent under water-limited conditions, and the effects of these QTLs and their interactions were examined in this research work. Full article
(This article belongs to the Special Issue Feature Papers in Genotype Evaluation and Breeding)
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11 pages, 1483 KiB  
Article
Assessing the Genotype-by-Environment G×E Interaction in Desi Chickpea via the Bayesian Additive Main Effects and Multiplicative Interaction Model
by Ajmalud Din, Rozina Gul, Hamayoon Khan, Julian Garcia-Abadillo Velasco, Reyna Persa, Julio Isidro y Sánchez and Diego Jarquin
Agriculture 2024, 14(2), 215; https://doi.org/10.3390/agriculture14020215 - 29 Jan 2024
Viewed by 1385
Abstract
Chickpea is the second most important legume crop in pulses, and its performance is greatly influenced by environmental factors inducing a change in the response patterns, complicating the selection of the best cultivar(s). The genotype-by-environment (G×E) patterns of a chickpea dataset (yield and [...] Read more.
Chickpea is the second most important legume crop in pulses, and its performance is greatly influenced by environmental factors inducing a change in the response patterns, complicating the selection of the best cultivar(s). The genotype-by-environment (G×E) patterns of a chickpea dataset (yield and days to emergence DTE) of 36 lines evaluated in 12 environments in Pakistan were assessed in this study. The interaction patterns were evaluated using the Bayesian Additive Main Effects and Multiplicative Interaction (AMMI) model. For yield, the 95% highest posterior density (HPD) regions showed that none of the genotypes (G) were found to be stable since these did not include the null point (0, 0), while for the environments, only E-8 and E-10 included the origin. In contrast, for DTE 11, genotypes included the null point being considered stable for this trait; however, none of the environments included the origin. These results suggest that considering both traits, the genotypes G2, G6, and G17 are the best genotypes across environments, while environments E-8 and E-10 were identified as favorable to all genotypes. Based on the obtained results, the abovementioned genotypes can be forwarded for further processing to be released as commercial varieties. Full article
(This article belongs to the Special Issue Feature Papers in Genotype Evaluation and Breeding)
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Review

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26 pages, 1318 KiB  
Review
Molecular Genetic Insights into the Stress Responses and Cultivation Management of Zoysiagrass: Illuminating the Pathways for Turf Improvement
by Lanshuo Wang, Yueyue Yuan and Jeongsik Kim
Agriculture 2024, 14(10), 1718; https://doi.org/10.3390/agriculture14101718 - 30 Sep 2024
Viewed by 601
Abstract
Zoysiagrass (Zoysia spp.) and its hybrids are known for their low maintenance requirements and are widely utilized as warm-season turfgrass, which offers considerable ecological, environmental, and economic benefits in various environments. Molecular genetic approaches, including the identification and genetic engineering of valuable [...] Read more.
Zoysiagrass (Zoysia spp.) and its hybrids are known for their low maintenance requirements and are widely utilized as warm-season turfgrass, which offers considerable ecological, environmental, and economic benefits in various environments. Molecular genetic approaches, including the identification and genetic engineering of valuable gene resources, present a promising opportunity to enhance the quality and performance of zoysiagrass. This review surveys the recent molecular genetic discoveries in zoysiagrass species, with a focus on elucidating plant responses to various abiotic and biotic stresses. Furthermore, this review explores the notable advancements in gene function exploration to reduce the maintenance demands of zoysiagrass cultivation. In addition, we discuss the achievements and potential of contemporary molecular and genetic tools, such as omics approaches and gene editing technologies, in developing zoysiagrass cultivars with desirable traits. Overall, this comprehensive review highlights future strategies that may leverage current molecular insights to accelerate zoysiagrass improvement and further promote sustainable turf management practices. Full article
(This article belongs to the Special Issue Feature Papers in Genotype Evaluation and Breeding)
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28 pages, 1739 KiB  
Review
Role of Genome Sequences of Major and Minor Millets in Strengthening Food and Nutritional Security for Future Generations
by Theivanayagam Maharajan, Thumadath Palayullaparambil Ajeesh Krishna, Neenthamadathil Mohandas Krishnakumar, Mani Vetriventhan, Himabindu Kudapa and Stanislaus Antony Ceasar
Agriculture 2024, 14(5), 670; https://doi.org/10.3390/agriculture14050670 - 25 Apr 2024
Cited by 7 | Viewed by 2417
Abstract
Millets are small-seeded cereals belonging to the family Poaceae. They are considered to be climate-resilient and future nutritional food cereals for humans. Millets are resistant to biotic and abiotic stressors compared to other major cereals and thrive in low-quality soils with little maintenance [...] Read more.
Millets are small-seeded cereals belonging to the family Poaceae. They are considered to be climate-resilient and future nutritional food cereals for humans. Millets are resistant to biotic and abiotic stressors compared to other major cereals and thrive in low-quality soils with little maintenance and less rainfall. The importance of millets is still not well known to many people due to the lack of popularity and cultivation in semi-arid tropics of Asia and Africa. The United Nations has declared 2023 as the International Year of Millets (IYM 2023) to promote millet cultivation and popularize their health benefits globally. A few years ago, the application of molecular biology was in its infancy in millets due to the unavailability of genome sequences. Genome sequences are available for most of the millets on NCBI and Phytozome databases. In this review, we discuss the details of genome sequences for millets, candidate genes identified from the native genome of millets. The current status of quantitative trait loci and genome-wide association studies in millets are also discussed. The utilization of millet genome sequences in functional genomics research and translating the information for crop improvement will help millet and non-millet cereals survive harsh environments in the future. Such efforts will help strengthen food security and reduce malnutrition worldwide in 2050. Full article
(This article belongs to the Special Issue Feature Papers in Genotype Evaluation and Breeding)
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