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Feature Papers in Genotype Evaluation and Breeding

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A special issue of Agriculture (ISSN 2077-0472). This special issue belongs to the section "Genotype Evaluation and Breeding".

Deadline for manuscript submissions: 5 September 2024 | Viewed by 5088

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Special Issue Editor

Prof. Dr. Rodomiro Ortiz

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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

Published Papers (5 papers)

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Research

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20 pages, 8175 KiB

Open AccessArticle

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://0-doi-org.brum.beds.ac.uk/10.3390/agriculture14050693 (registering DOI) - 28 Apr 2024

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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 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

Open AccessArticle

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://0-doi-org.brum.beds.ac.uk/10.3390/agriculture14030455 - 11 Mar 2024

Viewed by 2473

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 (T_i). The aim of this research was to determine whether tetrasomic genomic best linear unbiased predictors (GBLUPs) may facilitate selecting for tuber yield across early T_i 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

Open AccessArticle

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://0-doi-org.brum.beds.ac.uk/10.3390/agriculture14030431 - 07 Mar 2024

Viewed by 828

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 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

Open AccessArticle

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://0-doi-org.brum.beds.ac.uk/10.3390/agriculture14020215 - 29 Jan 2024

Viewed by 902

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 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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28 pages, 1739 KiB

Open AccessReview

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://0-doi-org.brum.beds.ac.uk/10.3390/agriculture14050670 - 25 Apr 2024

Viewed by 226

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 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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