Genomic selection methods for crop improvement: Current status and prospects

Plant breeders make selection decisions based on multiple traits, such as yield, plant height, flowering time, and disease resistance. A commonly used approach in multi-trait genomic selection is index selection, which assigns weights to different traits relative to their economic importance. However, classical index selection only optimizes genetic gain in the next generation, requires some experimentation to find weights that lead to desired outcomes, and has difficulty optimizing nonlinear breeding objectives. Multi-objective optimization has also been used to identify the Pareto frontier of selection decisions, which represents different trade-offs across multiple traits. We propose a new approach, which maximizes certain traits while keeping others within desirable ranges. Optimal selection decisions are made using a new version of the look-ahead selection (LAS) algorithm, which was recently proposed for single-trait genomic selection, and achieved superior performance with respect to other state-of-the-art selection methods. To demonstrate the effectiveness of the new method, a case study is developed using a realistic data set where our method is compared with conventional index selection. Results suggest that the multi-trait LAS is more effective at balancing multiple traits compared with index selection.

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Genetic Transformation of Apomictic Grasses: Progress and Constraints

Frontiers in Plant Science ◽

10.3389/fpls.2021.768393 ◽

2021 ◽

Vol 12 ◽

Author(s):

Andrés M. Bellido ◽

Eduado D. Souza Canadá ◽

Hugo R. Permingeat ◽

Viviana Echenique

Keyword(s):

Genetic Transformation ◽

Plant Transformation ◽

Large Scale ◽

Crop Improvement ◽

Current Status ◽

Grass Species ◽

Brachiaria Brizantha ◽

Apomictic Species ◽

Transformation Methods

The available methods for plant transformation and expansion beyond its limits remain especially critical for crop improvement. For grass species, this is even more critical, mainly due to drawbacks in in vitro regeneration. Despite the existence of many protocols in grasses to achieve genetic transformation through Agrobacterium or biolistic gene delivery, their efficiencies are genotype-dependent and still very low due to the recalcitrance of these species to in vitro regeneration. Many plant transformation facilities for cereals and other important crops may be found around the world in universities and enterprises, but this is not the case for apomictic species, many of which are C4 grasses. Moreover, apomixis (asexual reproduction by seeds) represents an additional constraint for breeding. However, the transformation of an apomictic clone is an attractive strategy, as the transgene is immediately fixed in a highly adapted genetic background, capable of large-scale clonal propagation. With the exception of some species like Brachiaria brizantha which is planted in approximately 100 M ha in Brazil, apomixis is almost non-present in economically important crops. However, as it is sometimes present in their wild relatives, the main goal is to transfer this trait to crops to fix heterosis. Until now this has been a difficult task, mainly because many aspects of apomixis are unknown. Over the last few years, many candidate genes have been identified and attempts have been made to characterize them functionally in Arabidopsis and rice. However, functional analysis in true apomictic species lags far behind, mainly due to the complexity of its genomes, of the trait itself, and the lack of efficient genetic transformation protocols. In this study, we review the current status of the in vitro culture and genetic transformation methods focusing on apomictic grasses, and the prospects for the application of new tools assayed in other related species, with two aims: to pave the way for discovering the molecular pathways involved in apomixis and to develop new capacities for breeding purposes because many of these grasses are important forage or biofuel resources.

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Accuracy of Genomic Selection Methods in a Standard Data Set of Loblolly Pine (Pinus taeda L.)

Genetics ◽

10.1534/genetics.111.137026 ◽

2012 ◽

Vol 190 (4) ◽

pp. 1503-1510 ◽

Cited By ~ 236

Author(s):

M. F. R. Resende ◽

P. Muñoz ◽

M. D. V. Resende ◽

D. J. Garrick ◽

R. L. Fernando ◽

...

Keyword(s):

Genomic Selection ◽

Pinus Taeda ◽

Loblolly Pine ◽

Selection Methods ◽

Data Set ◽

Standard Data ◽

Pinus Taeda L

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A comparison of genomic selection methods for breeding value prediction

Science Bulletin ◽

10.1007/s11434-015-0791-2 ◽

2015 ◽

Vol 60 (10) ◽

pp. 925-935 ◽

Cited By ~ 14

Author(s):

Xin Wang ◽

Zefeng Yang ◽

Chenwu Xu

Keyword(s):

Genomic Selection ◽

Breeding Value ◽

Selection Methods ◽

Value Prediction

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The Plant Genome special issue: Advances in genomic selection and application of machine learning in genomic prediction for crop improvement

The Plant Genome ◽

10.1002/tpg2.20178 ◽

2021 ◽

Author(s):

Rajeev K. Varshney

Keyword(s):

Machine Learning ◽

Genomic Selection ◽

Genomic Prediction ◽

Crop Improvement ◽

Plant Genome ◽

Special Issue

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Influence of Silicon on Biocontrol Strategies to Manage Biotic Stress for Crop Protection, Performance, and Improvement

Plants ◽

10.3390/plants10102163 ◽

2021 ◽

Vol 10 (10) ◽

pp. 2163

Author(s):

Krishan K. Verma ◽

Xiu-Peng Song ◽

Dan-Dan Tian ◽

Dao-Jun Guo ◽

Zhong-Liang Chen ◽

...

Keyword(s):

Biotic Stress ◽

Crop Improvement ◽

Crop Protection ◽

Essential Element ◽

Common Element ◽

Current Status ◽

Pest Infestation ◽

Recent Developments ◽

Term Basis ◽

Near Future

Silicon (Si) has never been acknowledged as a vital nutrient though it confers a crucial role in a variety of plants. Si may usually be expressed more clearly in Si-accumulating plants subjected to biotic stress. It safeguards several plant species from disease. It is considered as a common element in the lithosphere of up to 30% of soils, with most minerals and rocks containing silicon, and is classified as a “significant non-essential” element for plants. Plant roots absorb Si, which is subsequently transferred to the aboveground parts through transpiration stream. The soluble Si in cytosol activates metabolic processes that create jasmonic acid and herbivore-induced organic compounds in plants to extend their defense against biotic stressors. The soluble Si in the plant tissues also attracts natural predators and parasitoids during pest infestation to boost biological control, and it acts as a natural insect repellent. However, so far scientists, policymakers, and farmers have paid little attention to its usage as a pesticide. The recent developments in the era of genomics and metabolomics have opened a new window of knowledge in designing molecular strategies integrated with the role of Si in stress mitigation in plants. Accordingly, the present review summarizes the current status of Si-mediated plant defense against insect, fungal, and bacterial attacks. It was noted that the Si-application quenches biotic stress on a long-term basis, which could be beneficial for ecologically integrated strategy instead of using pesticides in the near future for crop improvement and to enhance productivity.

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CURRENT STATUS OF TRANSGENIC COTTON-UTILITY OF GENOTYPE INDEPENDENT IN PLANTA APPROACHES FOR THE GENERATION OF TRANSGENICS

International Journal on Agricultural Sciences ◽

10.53390/ijas.v11i2.6 ◽

2020 ◽

Vol 11 (2) ◽

Author(s):

Kesiraju Karthik

Keyword(s):

Tissue Culture ◽

In Vitro Regeneration ◽

Crop Improvement ◽

Transgenic Cotton ◽

Current Status ◽

In Planta ◽

Biotic And Abiotic Stresses ◽

Independent Manner ◽

Gossypium Spp

Cotton (Gossypium spp.), is a mercantile crop plant is grown for its fluffy fiber and cotton seed oil in around 70 countries worldwide. Cotton is an economically important crop, shows erratic productivity under rain feed conditions; it is bogged down with many biotic and abiotic stresses. Due to lack of resistant germplasm, crop improvement through conventional breeding practices has been lagging. Genetic engineering offers numerous protocols to engineer plants to overcome stress. Biotechnological intervention for cotton improvement has begun three decades ago. The recalcitrance of cotton to tissue culture has been the major constraint for in vitro regeneration. Alternate methods that evade tissue culture regeneration steps have thus been envisaged. Till date there are very few standardized protocols that can be employed to develop transgenics in a genotype independent manner. Thus, genotype independent in planta transformation strategies have gained momentum in the present days, but reproducibility of reported protocols remains an amigna in many cases. In planta transformations holds prominence due to viability and ease in generation of transgenic cotton plants with in less time. This review focuses on grouping efforts made by different research groups in this senior. Several reports and standardizations have been focused that reports development of transgenic cotton.

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Current status of taro (Colocasia esculenta) utilization as local food diversification toward climate resilience in Indonesia

IOP Conference Series Earth and Environmental Science ◽

10.1088/1755-1315/913/1/012027 ◽

2021 ◽

Vol 913 (1) ◽

pp. 012027

Author(s):

D Maretta ◽

Sobir ◽

I Helianti ◽

Purwono ◽

E Santosa

Keyword(s):

Climate Change ◽

Value Chain ◽

Local Food ◽

Negative Impact ◽

Group Discussion ◽

Crop Improvement ◽

Current Status ◽

Tropical Country ◽

Impact Of Climate Change ◽

The Impact

Abstract Indonesia is a tropical country that experiences the impact of climate change. The utilization of taro as an amphibian crop might sustain the food availability for the most vulnerable farmers against the negative impact of climate change. The study aims to evaluate the current status of taro utilization and production as local food concerning food diversification, sustainable agriculture, and climate change issues. Data were obtained from a focus group discussion with primary stakeholders of the taro value chain and literature review. Results show that taro is an important secondary food in some regions with three main uses as local consumption, local trading, and export. Prominent taro consumers existed in West Papua, Papua, Maluku, and Central Sulawesi Provinces with consumption rates 10.6, 5.3, 2.2, and 2.0 kg/capita/year, respectively. Taro was intensively cultivated in Banten, West Java, and South Sulawesi provinces, for fresh and processed products. The respondents agree with taro as a prospective adaptive crop to climate change of both drought and excess precipitation. There are some issues in the biodiversity conservation, crop improvement, link-match industry, and stakeholder capacity building for competitive, quality, quantity, and sustainable production, as future works in the taro value chain in Indonesia.

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