Enhancing genetic gain through the application of genomic selection in developing irrigated rice for the favorable ecosystem in Bangladesh

Genome-Wide Association Study and Genomic Prediction of Soft Wheat End-Use Quality Traits Under Post-Anthesis Heat-Stressed Conditions

Wheat end-use quality is an important component of a wheat breeding program. Heat stress during grain filling impacts wheat quality traits, making it crucial to understand the genetic basis of wheat quality traits under post-anthesis heat stress. This study aimed to identify the genomic regions associated with wheat quality traits using genome-wide association studies (GWASs) and evaluate the prediction accuracy of different genomic selection (GS) models. A panel of 236 soft red facultative wheat genotypes was evaluated for end-use quality traits across four heat-stressed environments over three years. Significant phenotypic variation was observed across environments for traits such as grain yield (GY), grain protein (GP), grain hardness (GH), and flour yield (AFY). Heritability estimates ranged from 0.52 (GY) to 0.91 (GH). The GWASs revealed 136 significant marker-trait associations (MTAs) across all 21 chromosomes, with several MTAs located within candidate genes involved in stress responses and quality traits. Genomic selection models showed prediction accuracy values up to 0.60, with within-environment prediction outperforming across-environment prediction. These results suggest that integrating GWAS and GS approaches can enhance the selection of wheat quality traits under heat stress, contributing to the development of heat-tolerant varieties.

Stochastic simulation to optimize rice breeding at IRRI

Introduction

Genetic improvement in rice increased yield potential and improved varieties for farmers over the last decades. However, the demand for rice is growing while its cultivation faces challenges posed by climate change. To address these challenges, rice breeding programs need to adopt efficient breeding strategies to provide a steady increase in the rate of genetic gain for major traits. The International Rice Research Institute (IRRI) breeding program has evolved over time to implement faster and more efficient breeding techniques such as rapid generation advance (RGA) and genomic selection (GS). Simulation experiments support data-driven optimization of the breeding program toward the desired rate of genetic gain for key traits.

Methods

This study used stochastic simulations to compare breeding schemes with different cycle times. The objective was to assess the impact of different genomic selection strategies on medium- and long-term genetic gain. Four genomic selection schemes were simulated, representing the past approaches (5 years recycling), current schemes (3 years recycling), and two options for the future schemes (both with 2 years recycling).

Results

The 2-Year within-cohort prediction scheme showed a significant increase in genetic gain in the medium-term horizon. Specifically, it resulted in a 22%, 24%, and 27% increase over the current scheme in the zero, intermediate, and high genotype-by-environment interaction (GEI) contexts, respectively. On the other hand, the 2-Year scheme based on between-cohort prediction was more efficient in the long term, but only in the absence of GEI. Consistent with our expectations, the shortest breeding schemes showed an increase in genetic gain and faster depletion of genetic variance compared to the current scheme.

Discussion

These results suggest that higher rates of genetic gain are achievable in the breeding program by further reducing the cycle time and adjusting the target population of environments. However, more attention is needed regarding the crossing strategy to use genetic variance optimally.

Genetic Gain and Inbreeding in Different Simulated Genomic Selection Schemes for Grain Yield and Oil Content in Safflower

Safflower (Carthamus tinctorius L.) is a multipurpose minor crop consumed by developed and developing nations around the world with limited research funding and genetic resources. Genomic selection (GS) is an effective modern breeding tool that can help to fast-track the genetic diversity preserved in genebank collections to facilitate rapid and efficient germplasm improvement and variety development. In the present study, we simulated four GS strategies to compare genetic gains and inbreeding during breeding cycles in a safflower recurrent selection breeding program targeting grain yield (GY) and seed oil content (OL). We observed positive genetic gains over cycles in all four GS strategies, where the first cycle delivered the largest genetic gain. Single-trait GS strategies had the greatest gain for the target trait but had very limited genetic improvement for the other trait. Simultaneous selection for GY and OL via indices indicated higher gains for both traits than crossing between the two single-trait independent culling strategies. The multi-trait GS strategy with mating relationship control (GS_GY + OL + Rel) resulted in a lower inbreeding coefficeint but a similar gain compared to that of the GS_GY + OL (without inbreeding control) strategy after a few cycles. Our findings lay the foundation for future safflower GS breeding.

Validation of sorghum quality control (QC) markers across African breeding lines

Sorghum [Sorghum bicolor (L.) Moench] is a cereal crop of critical importance in the semi-arid tropics, particularly in Africa where it is second only to maize (Zea mays L.) by area of cultivation. The International Crops Research Institute for the Semi-Arid Tropics sorghum breeding program for Eastern and Southern Africa is the largest in the region and develops improved varieties for target agro-ecologies. Varietal purity and correct confirmation of new crosses are essential for the integrity and efficiency of a breeding program. We used 49 quality control (QC) kompetitive allele-specific PCR single nucleotide polymorphism (SNP) markers to genotype 716 breeding lines. Note that 46 SNPs were polymorphic with the top 10 most informative revealing polymorphism information content (PIC), minor allele frequency (MAF), and observed heterozygosity (Ho) of 0.37, 0.43, and 0.02, respectively, and explaining 45% of genetic variance within the first two principal components (PC). Thirty-nine markers were highly informative across 16 Burkina Faso breeding lines, out of which the top 10 revealed average PIC, MAF, and Ho of 0.36, 0.39, and 0.05, respectively. Discriminant analysis of principal components done using top 30 markers separated the breeding lines into five major clusters, three of which were distinct. Six of the top 10 most informative markers successfully confirmed hybridization of crosses between genotypes IESV240, KARIMTAMA1, F6YQ212, and FRAMIDA. A set of 10, 20, and 30 most informative markers are recommended for routine QC applications. Future effort should focus on the deployment of these markers in breeding programs for enhanced genetic gain.

Genomic selection in plant breeding: Key factors shaping two decades of progress

Genomic selection, the application of genomic prediction (GP) models to select candidate individuals, has significantly advanced in the past two decades, effectively accelerating genetic gains in plant breeding. This article provides a holistic overview of key factors that have influenced GP in plant breeding during this period. We delved into the pivotal roles of training population size and genetic diversity, and their relationship with the breeding population, in determining GP accuracy. Special emphasis was placed on optimizing training population size. We explored its benefits and the associated diminishing returns beyond an optimum size. This was done while considering the balance between resource allocation and maximizing prediction accuracy through current optimization algorithms. The density and distribution of single-nucleotide polymorphisms, level of linkage disequilibrium, genetic complexity, trait heritability, statistical machine-learning methods, and non-additive effects are the other vital factors. Using wheat, maize, and potato as examples, we summarize the effect of these factors on the accuracy of GP for various traits. The search for high accuracy in GP-theoretically reaching one when using the Pearson's correlation as a metric-is an active research area as yet far from optimal for various traits. We hypothesize that with ultra-high sizes of genotypic and phenotypic datasets, effective training population optimization methods and support from other omics approaches (transcriptomics, metabolomics and proteomics) coupled with deep-learning algorithms could overcome the boundaries of current limitations to achieve the highest possible prediction accuracy, making genomic selection an effective tool in plant breeding.

Realized Genetic Gain in Rice: Achievements from Breeding Programs

Genetic improvement is crucial for ensuring food security globally. Indeed, plant breeding has contributed significantly to increasing the productivity of major crops, including rice, over the last century. Evaluating the efficiency of breeding strategies necessitates a quantification of this progress. One approach involves assessing the genetic gain achieved through breeding programs based on quantitative traits. This study aims to provide a theoretical understanding of genetic gain, summarize the major results of genetic gain studies in rice breeding, and suggest ways of improving breeding program strategies and future studies on genetic gain. To achieve this, we present the concept of genetic gain and the essential aspects of its estimation. We also provide an extensive literature review of genetic gain studies in rice (Oryza sativa L.) breeding programs to understand the advances made to date. We reviewed 29 studies conducted between 1999 and 2023, covering different regions, traits, periods, and estimation methods. The genetic gain for grain yield, in particular, showed significant variation, ranging from 1.5 to 167.6 kg/ha/year, with a mean value of 36.3 kg/ha/year. This translated into a rate of genetic gain for grain yield ranging from 0.1% to over 3.0%. The impact of multi-trait selection on grain yield was clarified by studies that reported genetic gains for other traits, such as plant height, days to flowering, and grain quality. These findings reveal that while breeding programs have achieved significant gains, further improvements are necessary to meet the growing demand for rice. We also highlight the limitations of these studies, which hinder accurate estimations of genetic gain. In conclusion, we offer suggestions for improving the estimation of genetic gain based on quantitative genetic principles and computer simulations to optimize rice breeding strategies.