Genetic Improvement Programs Research Articles

A high-quality chromosome-level genome assembly of rohu carp, Labeo rohita, and its utilization in SNP-based exploration of gene flow and sex determination.

Labeo rohita (rohu) is a carp important to aquaculture in South Asia, with a production volume close to Atlantic salmon. While genetic improvements to rohu are ongoing, the genomic methods commonly used in other aquaculture improvement programs have historically been precluded in rohu, partially due to the lack of a high-quality reference genome. Here we present a high-quality de novo genome produced using a combination of next-generation sequencing technologies, resulting in a 946 Mb genome consisting of 25 chromosomes and 2,844 unplaced scaffolds. Notably, while approximately half the size of the existing genome sequence, our genome represents 97.9% of the genome size newly estimated here using flow cytometry. Sequencing from 120 individuals was used in conjunction with this genome to predict the population structure, diversity, and divergence in three major rivers (Jamuna, Padma, and Halda), in addition to infer a likely sex determination mechism in rohu. These results demonstrate the utility of the new rohu genome in modernizing some aspects of rohu genetic improvement programs.

Gene Editing for Plant Resistance to Abiotic Factors: A Systematic Review.

Agricultural crops are exposed to various abiotic stresses, such as salinity, water deficits, temperature extremes, floods, radiation, and metal toxicity. To overcome these challenges, breeding programs seek to improve methods and techniques. Gene editing by Clustered Regularly Interspaced Short Palindromic Repeats-CRISPR/Cas-is a versatile tool for editing in all layers of the central dogma with focus on the development of cultivars of plants resistant or tolerant to multiple biotic or abiotic stresses. This systematic review (SR) brings new contributions to the study of the use of CRISPR/Cas in gene editing for tolerance to abiotic stress in plants. Articles deposited in different electronic databases, using a search string and predefined inclusion and exclusion criteria, were evaluated. This SR demonstrates that the CRISPR/Cas system has been applied to several plant species to promote tolerance to the main abiotic stresses. Among the most studied crops are rice and Arabidopsis thaliana, an important staple food for the population, and a model plant in genetics/biotechnology, respectively, and more recently tomato, whose number of studies has increased since 2021. Most studies were conducted in Asia, specifically in China. The Cas9 enzyme is used in most articles, and only Cas12a is used as an additional gene editing tool in plants. Ribonucleoproteins (RNPs) have emerged as a DNA-free strategy for genome editing without exogenous DNA. This SR also identifies several genes edited by CRISPR/Cas, and it also shows that plant responses to stress factors are mediated by many complex-signaling pathways. In addition, the quality of the articles included in this SR was validated by a risk of bias analysis. The information gathered in this SR helps to understand the current state of CRISPR/Cas in the editing of genes and noncoding sequences, which plays a key role in the regulation of various biological processes and the tolerance to multiple abiotic stresses, with potential for use in plant genetic improvement programs.

Genomic evaluation of carcass traits of Korean beef cattle Hanwoo using a single-step marker effect model

Hanwoo beef cattle are well known for the flavor and tenderness of their meat. Genetic improvement programs have been extremely successful over the last 40 yr. Recently, genomic selection was initiated in Hanwoo to enhance genetic progress. Routine genomic evaluation based on the single-step breeding value model was implemented in 2020 for all economically important traits. In this study, we tested a single-step marker effect model for the genomic evaluation of four carcass traits, namely, carcass weight (CW), eye muscle area, backfat thickness, and marbling score. In total, 8,023,666 animals with carcass records were jointly evaluated, including 29,965 genotyped animals. To assess the prediction stability of the single-step model, carcass data from the last 4 yr were removed in a forward validation study. The estimated genomic breeding values (GEBV) of the validation animals and other animals were compared between the truncated and full evaluations. A parallel conventional best linear unbiased prediction (BLUP) evaluation with either the full or the truncated dataset was also conducted for comparison with the single-step model. The estimates of the marker effect from the truncated evaluation were highly correlated with those from the full evaluation, ranging from 0.88 to 0.92. The regression coefficients of the estimates of the marker effect for the full and truncated evaluations were close to their expected value of 1, indicating unbiased estimates for all carcass traits. Estimates of the marker effect revealed three chromosomal regions (chromosomes 4, 6, and 14) harboring the major genes for CW in Hanwoo. For validation of cows or steers, the single-step model had a much higher R2 value for the linear regression model than the conventional BLUP model. Based on the regression intercept and slope of the validation, the single-step evaluation was neither inflated nor deflated. For genotyped animals, the estimated GEBV from the full and truncated evaluations were more correlated than the estimated breeding values from the two conventional BLUP evaluations. The single-step model provided a more accurate and stable evaluation over time.

Whole-genome resequencing reveals recent signatures of selection in five populations of largemouth bass ( Micropterus salmoides).

Largemouth bass ( Micropterus salmoides) is an economically important fish species in North America, Europe, and China. Various genetic improvement programs and domestication processes have modified its genome sequence through selective pressure, leaving nucleotide signals that can be detected at the genomic level. In this study, we sequenced 149 largemouth bass fish, including protospecies (imported from the US) and improved breeds (four domestic breeding populations from China). We detected genomic regions harboring certain genes associated with improved traits, which may be useful molecular markers for practical domestication, breeding, and selection. Subsequent analyses of genetic diversity and population structure revealed that the improved breeds have undergone more rigorous genetic changes. Through selective signal analysis, we identified hundreds of putative selective sweep regions in each largemouth bass line. Interestingly, we predicted 103 putative candidate genes potentially subjected to selection, including several associated with growth (p sst1 and grb10), early development ( klf9, sp4, and sp8), and immune traits ( pkn2, sept2, bcl6, and ripk2). These candidate genes represent potential genomic landmarks that could be used to improve important traits of biological and commercial interest. In summary, this study provides a genome-wide map of genetic variations and selection footprints in largemouth bass, which may benefit genetic studies and accelerate genetic improvement of this economically important fish.

Evaluation of heritability and selection response of the growth in the first-generation population of gourami (Osphronemus goramy Lac.) originated from four populations

The genetic improvement program through selective breeding is one of the efforts to overcome the slow-growing constraints in gourami (Osphronemus goramy Lac.) farming. The selective breeding to improve the growth performance of gourami using the family selection method was first conducted by the formation of a base population using a diallele cross of four populations originating from Kalimantan (Borneo), Jambi, Majalengka, and Tasikmalaya. The best performing individuals were selected to produce the first generation (F1) population. This study aimed to evaluate the growth (body weight) and determine the heritability of the F1 population. Individuals selected from the base population were communally spawned using a half-sib mating with a male:female ratio of 1:2. The grow-out phase was carried out in earthen ponds with a stocking density of 5 fish/m2, 7 families out of 14 families were kept until 13 months of age. The results showed that the body weight variation coefficient ranged from 12.36-18.65% with a selection differential of 70.75 - 112.56 g. The heritability of the body weight was 0.88, with a selection response of 11.18%. These results revealed the selection progress with increased body weight in F1 population. Thus, selective breeding is effective to be continued.

Comprehensive genetic analysis of linear type traits for characterization of the Sahiwal cattle in an organized herd

Sahiwal is one of the most important dairy cattle breeds of the Indian subcontinent. A holistic and balanced approach to selection and breeding strategies must be adopted to bring about desirable genetic improvement in livestock, including indigenous cattle. The inclusion of linear type traits for dairy cattle selection in any breed improvement program has not been carried out in India so far. Therefore, this study was taken up to characterize Sahiwal cattle, on the basis of linear type traits. Data was collected on adult Sahiwal cows up to their 10thparity, maintained at Institute herd of Indian Council of Agricultural Research- National Dairy Research Institute, Karnal, Haryana from 2006-2021. Data were analysed using Least Squares Maximum Likelihood (LSMLMW), considering a sire model for the present study. Parity, season and period of calving were taken as fixed effect and age at first calving as covariable. Sire or animal was considered as random variable. Least squares means of objective linear type traits viz., stature was 125.97±0.68 cm, body length 136.58±1.01 cm, chest girth 173.04±1.14 cm, body depth203.40± 1.39 cm, rump angle 14.50±0.39 cm, rump width 20.62±0.28cm, udder depth 20.87±0.41 cm, rear udder height 18.38±0.33 cm, and teat length 6.16±0.24 cm. On the other hand, least square mean scores of subjective linear type traits (1-9 scale) viz. fore teat placement was 6.32±0.46, rear teat placement was 7.27±0.35,rear leg side view was 6.26±0.26, rear leg rear view was 6.28±0.27score, foot angle 6.86±0.27, angularity 34.97±0.50-degree, central ligament 6.55± 0.39, fore udder attachment 5.91±0.32, fore teat placement 6.32±0.46, and rear teat placement was 7.27±0.35. Parity had a significant (p<0.05) effect on fore udder attachment and central ligament and teat length in Sahiwal cattle. Season of calving had the significant (p< 0.05) effect, observed in case of udder depth in Sahiwal cattle. Period of calving had a significant(p<0.05) effect on rump angle, udder depth, teat length, angularity and central ligament in Sahiwal cattle. Based on results of present study, it was observed that Sahiwal cattle establishes a balance between the scoring pattern of linear type traits, as the balance scoring of animals was desirable for better sustainability and production performance of a dairy cattle, on a longer run. Moreover, linear type traits have a better scope in selection process and genetic improvement programs that can be utilized as balanced and comprehensive approach for indigenous dairy cattle.

Utilization of Biotechnology, Neurotransmitter and Cytogenetic Indices in Selecting Pigeon Breeds

Investigations into LDH-A and DR-D4 genes polymorphism, neurotransmitter values and cytogenetic indices of 3 sexed pigeon breeds; non-racing pigeons, (wild rock), racing long distances pigeons (Jan Aarden) and racing short distances pigeons (Janssen) have been performed. The long-distances pigeon showed the highest brain neurotransmitters concentration (p<0.001) among pigeon breeds. Both LDH-A and DR-D4 genes polymorphism indicate the presence of different biodiversity values among pigeon breeds. The variations appeared on the position length 389bp for LDH-A polymorphism, and on two positions length of 418bp and 524bp for DR-D4 polymorphism of long distances male pigeon indicate the presence of unique diversity and overall differences in the amino acids structure in this breed. The protein sequence of both genes showed that in the position of 60 for LDH-A gene the amino acid K (lys) was converted to E (glu), while, in the positions of 117 and 153 for DR-D4 gene the amino acid R (arg) and L (leu) were converted to S (ser) and F (phe) only in long distances male pigeon compared to the other breeds. Moreover, there were slight differences in cytogenetic indices detected among the three pigeon breeds. It can be concluded that both DR-D4 and LDH-A genes polymorphism and neurotransmitters estimations in the brain tissue of racing pigeon would be useful indices for the differentiation and genetic characterization of pigeon breeds and provide a foundation for developing sustainable genetic improvement and conservation programs of the breeding and selecting racing pigeon breeders.

1930‒1990 - THE INTERVENTION OF THE BRAZILIAN STATE IN THE SUGAR-ENERGY SECTOR: IAA-PLANALSUCAR, PROÁLCOOL AND THE PARTICIPATION OF GILBERTO MILLER AZZI. DID WORK?

In Brazil, sugarcane is the crop whose agro-industrial development has taken the longest path and has the greatest prominence in the national agro-industry, without precedent. With 500 years of history, Brazil is today the largest producer of sugarcane raw material and sugarcane ethanol in the world. In addition, has the world's largest program for the replacement of fossil fuel by ethanol in vehicles and shares with India the position of largest sugar producer; in addition, it has developed the largest active sugarcane genetic improvement program in the world. However, in contrast to these achievements throughout its history, it has also received criticism even from businesspersons of the sector itself, mainly regarding State intervention and its inefficiency. This is a paradox: “success and inefficiency?” The general objective of this work was to analyze exactly this contradiction since the great agro-industrial development occurred especially during the 60 years of State intervention (1930‒1990). We concluded that this intervention was a key element in the success of the agroindustry both during and after the intervention. Many personalities deserve mention in this process, in both the field of ideas and decisions and practical actions: politicians, public agents, businesspersons, sugar mill owners, agroindustry technicians, and independent producers. We selected a researcher, Dr. Gilberto Miller Azzi, as an example, due to the fact that, from 1955 onwards, as a researcher at the IAA, he represented the scientific and technological area of the Brazilian State, acting decisively for the achievements of the sector. In this regard, an analysis was made of the main factors that have leveraged the national sugar and alcohol sector from the 1930s to the present day.

Caracterização agronômica e interação genótipo ambiente de quinoa nas condições do Brasil e da Colômbia

ABSTRACT Quinoa is a highly adaptable crop due to its considerable genetic variability, making it an important trait for cultivation under different soil and climatic conditions. To achieve crop-wide adaptation, it is essential to identify variability based on morpho-agronomic differences and genotype x environment (GxE) interaction. This study aimed to characterize eight quinoa progenies in Brazil and Colombia. The experiments in Brazil were conducted in an irrigated area of the Fazenda Água Limpa, Universidade de Brasília, at 1,100 m, on two dates: March to July 2018 and May to August 2019. In Colombia, experiments were carried out in Santander de Quilichao and Popayán at 1,100 and 1,800 m, respectively. The treatments consisted of five progenies selected in Brazil, one from Colombia, and two from Ecuador. The experiments followed a complete randomized block design, with eight progenies and four replications. For statistical analysis, the F test was used with p≤0.01 and p≤0.05. Means were grouped by the Scott-Knott test. The AMMI (Additive Main effects and Multiplicative Interaction) analysis was performed, combining analysis of variance and analysis of principal components, to adjust the main effects of genotypes (G) and environments (E) and the GxE interaction. Significant differences were found at p≤0.01 and p≤0.05 for environments, genotypes, and the interaction of GxE. The progenies with wide adaptation to environments were BRX2, BRX5, BRX6 (selected from BRS Syetetuba) and PRIX (selected from Piartal), with average yields above 3,151.95 kg/ha. The genotypes showed differences at the same location in different periods, expressing the need to carry out selection for specific periods and locations. Genotypes BRX5 and BRX6 showed high agronomic potential in all evaluated environments, being promising for future genetic improvement programs.

50 years of rice breeding in Bangladesh: genetic yield trends

To assess the efficiency of genetic improvement programs, it is essential to assess the genetic trend in long-term data. The present study estimates the genetic trends for grain yield of rice varieties released between 1970 and 2020 by the Bangladesh Rice Research Institute. The yield of the varieties was assessed from 2001–2002 to 2020–2021 in multi-locations trials. In such a series of trials, yield may increase over time due to (i) genetic improvement (genetic trend) and (ii) improved management or favorable climate change (agronomic/non-genetic trend). In both the winter and monsoon seasons, we observed positive genetic and non-genetic trends. The annual genetic trend for grain yield in both winter and monsoon rice varieties was 0.01 t ha−1, while the non-genetic trend for both seasons was 0.02 t ha−1, corresponding to yearly genetic gains of 0.28% and 0.18% in winter and monsoon seasons, respectively. The overall percentage yield change from 1970 until 2020 for winter rice was 40.96%, of which 13.91% was genetic trend and 27.05% was non-genetic. For the monsoon season, the overall percentage change from 1973 until 2020 was 38.39%, of which genetic and non-genetic increases were 8.36% and 30.03%, respectively. Overall, the contribution of non-genetic trend is larger than genetic trend both for winter and monsoon seasons. These results suggest that limited progress has been made in improving yield in Bangladeshi rice breeding programs over the last 50 years. Breeding programs need to be modernized to deliver sufficient genetic gains in the future to sustain Bangladeshi food security.

Climate Change's Impact on Agriculture and Food Security: An Opportunity to Showcase African Animal Genetic Resources

One of the current issues facing humanity is ensuring sustained global food security in the face of devastating effects of climate change; this challenge is particularly pressing on the African continent. Here, I present an opinion piece identifying local animal genetic resources as "African leverage point" that provide the highest chances to cushion rural fork to climate change, enhance environmental sustainability and food security in Africa. When it comes to boosting food production, coping with climate change, or bolstering the delivery of a wide range of ecosystem services, I believe that African animal genetic resources are essential alternatives for the sustainable growth of the livestock industry and its contribution to food security. Africa needs to address the support and development of indigenous animal genetic resources in order to meet the basic food needs of more than 1 billion people, address numerous environmental issues with continental implications, and focus on more effective and resilient food systems with the greatest impact on food security. The indigenous animal resources diversity and support actions to this unique group could provide a boost in protein that is lacking to constitute healthy diets in Africa. The priorities of nonprofit organizations, foundations, governments, citizens' groups, and companies can be influenced by this leverage point in the African food system. Due to continuous food insecurity, which appears to be becoming worse with climate change and makes it even harder to accomplish the SDGs on the continent, Africa has paid a hefty price for being misled about the worth of its own animal genetic resources. To the contrary, it is highly improbable that a strategy to improve food security and rural livelihoods that undermines the utilization of indigenous animal genetic resources will be viable in long-term. If Africa makes an effort, is committed, and fully commits resources to putting indigenous animal genetic resources at the forefront of combating food insecurity and accelerating the achievement of SDGs, it can achieve more under the adverse prevailing climate change induce environmental conditions. Our personal opinion is that we would not have had the ongoing food problems, even in the face of climate change, if Africa had over the years implemented the necessary mechanisms to develop and promote local animal genetic resources. What lies ahead in terms of climate change effect on food security in Africa is anyone's guess – but whatever it is, promoting continental adapted indigenous animal genetic resources portfolio is ready to handle it. Development and promotion of African animal genetic resources should be part of a continental strategy to transform smallholder animal production by 2050, in line with the goals of achieving the SGDs, to improve rural household food security, and bringing rural economy prosperity, resilience, sustainability, and all other desired animal related food outcomes for rural healthy diets. African animal genetic resources are the most important but underutilized resource to address the issue of ongoing food insecurity. The responsible use of local animal genetic resources through climate smart animal husbandry practices also contributes to food security, rural development and increased employment opportunities. African genetic improvement programs involving indigenous animal genetic resources must be considered as regards to local agriculture and livestock development aspirations, appropriateness to local reality and livelihood security, as well as environmental friendliness. Animal agriculture will fill in the enormous gaps in the continent's food supply if this animal group receives adequate attention and is used integrated properly in crop and livestock systems which characterize smallholder farming sector in Africa. Because they have evolved over time to accommodate the various climatic conditions and environmental pressures on the continent, Africa's native animal genetic resources are particularly resilient. Indirectly, the impact of climate change offers a chance to use native animal genetics from Africa. The use of local animal genetic diversity has the potential to substantially improve Africa's food security landscape hence should be given special consideration for sociocultural, environmental, and economic aspects, and with regard for smallholder farmer-specific factors of interest. African animal genetic resources have contributed significantly to the food and nutrition security aspects of the millions of people in their communities of origin and custody in Africa. The purpose of the perception piece is to educate the reader about the fundamental mechanisms that control the use of continental animal genetic resources and how the outlook for these mechanisms can be manipulated in the future for the benefit of improving food security in Africa. The discussion provides in-depth insight into the pertinent literature in understanding the significance of local animal genetic resources in terms of their contribution to food security in Africa.

Production of seeds and seedlings in the no-tillage system of vegetables: a systematic review

Direct Planting is a process of sowing in a non-turbulent soil, in which the seed or seedling is placed in furrows or pits, wide and deep enough to obtain an adequate coverage and a good contact of the seed with the soil. Breaking this dependence, there will be the fixation of the farmer in the field, through the reduction of production costs, improvement of the physical, chemical and biological conditions of the soil, greater sustainability of the system and improvement in the farmer's quality of life. Before implementing this system it is necessary to pay attention to a few details. The production of vegetable seeds is a very specialized activity, usually performed by companies with high technological and infrastructure levels. Its success is directly linked to three important factors: a) availability of cultivars, usually from genetic improvement programs, either public or private; b) specific climatic conditions for each species); and c) production technology. All these factors will influence the achievement of high quality seeds, in genetic, physiological, physical or sanitary aspects.

Morphoagronomic characterization of accessions of Triticum aestivum L.

Wheat is one of the most economically important cereals for the Department of Boyacá; however, the cultivated area sees low yields, phytosanitary problems, and a lack of genetic materials with desirable agronomic characteristics. The present study aimed to morphoagronomically characterize 49 accessions from the FENALCE germplasm bank using morphological and yield descriptors and multivariate and cluster analyses. The variables auricle color, edge shape, precocity, growth habit, grain size and serosity showed little genetic variability, while the number of tillers per plant, number of spikelets per spike and glume color showed high genetic variability. The principal component analysis, based on the correlation matrix, showed that the first four principal components (PC) explained 71% of the total variation observed in the characterized accessions. The cluster analysis formed three groups according to the evaluated morphological characteristics, with group three containing the accessions with the best agronomic characteristics. None of the evaluated accessions had rust damage. Around 15 wheat accessions had good agronomic performance under the conditions of this study, which should be used in future genetic improvement programs aimed at identifying elite materials in the Department of Boyacá.

Anatomic Leaf Structure of 'Sunrise Solo' and 'Golden THB' Papaya Plants

Papaya (Carica papaya L.) stands out as a strong economic driver, being one of the fruit trees that most contribute to the total volume of brazilian production. The description of leaf characteristics allows to understand structures that act in resistance to pathogens, relationships with water resources and photosynthetic of plants, in addition to contributing to genetic improvement programs. However, there are few studies that attempt to describe the leaf anatomy of the different papaya cultivars. Thus, this study aims to describe the main leaf structure of papaya cultivars Sunrise Solo and Golden THB. The leaves were collected in the municipalities of São Mateus and Aracruz, located in the north of the State of Espírito Santo, using transversal and paradermic sections and the usual techniques of plant histology. Both cultivars presented uni-stratified epidermis, followed by palisade chlorophyll parenchyma and lacunous with collateral vascular system. Calcium oxalate druses were more observed in the Sunrise Soil cultivar. The differences between cultivars were in the number of layers of mesophyll tissues.

Multi-trait Bayesian analysis and genetic parameter estimates in production characters of Mecheri sheep of India

The present study was carried out to estimate the genetic parameters for direct and maternal influences on Mecheri sheep (Ovis aries) growth traits using Bayesian multi-trait animal model. The genetic parameters were calculated using data from 2825 Mecheri lambs born between 2010 and 2020 that were kept in semi-arid tropical climate. Mecheri sheep body weight (mean ± SE) at various stages, viz. BW, WW, and BW12, were 2.6 ± 0.01, 11.1 ± 0.05, and 20.7 ± 0.13kg, respectively. The Mecheri sheep gained 71.5 percent of their body weight at the age of 6months. With the exception of birth weight, the weights of the animals varied considerably (P < 0.01) by the year of birth. The fixed effect of sex significantly (P < 0.01) influenced all the growth traits examined. The direct estimates of heritability (± SD) for BW, WW, BW6, and BW12 was 0.21 ± 0.041, 0.21 ± 0.041, 0.12 ± 0.052, and 0.13 ± 0.053, respectively, and the maternal heritability for BW, WW, BW6, and BW12 was 0.18 ± 0.021, 0.08 ± 0.023, 0.11 ± 0.022, and 0.13 ± 0.033, respectively. Significant variance was indicated by moderately larger direct heritability estimates for BWT and WWT, indicating that there will be more opportunities for selection response during the genetic improvement programme. For the majority of the variables examined, direct heritability values were higher than maternal heritability values. The additive genetic correlation between WW and BW6, BW9, and BW12 was 0.70 ± 0.145, 0.57 ± 0.171, and 0.50 ± 0.194, respectively. The maternal genetic correlations ranged from 0.06 ± 0.152 (BW-BW12) to 0.86 ± 0.046 (BW6-BW9), and the residual correlation varied from 0.18 ± 0.034 (BW-WW) to 0.85 ± 0.013 (BW9-BW12). The BW had a stronger genetic relationship with WW and a weaker relationship with other growth traits. The WW and BW6 showed a favourable genetic relationship, even if the tendency was decreasing in the latter stages of maturation. The BW6 and BW9 demonstrated the strongest positive genetic relationship (0.90 ± 0.052) of all the variables analysed. After examining the heritabilities and genetic correlation between WW and BW6, it was established that selection based on at WW was beneficial, since it manifests early in life and would result in moderate genetic progress through selection.

On-farm performance of genetically-improved rohu (Labeo rohita) in Bangladesh

IntroductionRohu (Labeo rohita Hamilton) is a globally significant aquaculture species for which genetically improved strains are increasingly available. In 2020, a multiplier population, comprised of highly–ranked generation-three (G3) families from the WorldFish Rohu Genetic Improvement Program, was released to hatcheries in Bangladesh for development into broodstock.MethodsTo estimate realised genetic gain for harvest weight in the G3-multiplier population, one pond from each of 19 Bangladeshi semi-commercial farms (ten in Jashore and nine in Natore–Rajshahi districts) were stocked with equal numbers of tagged fish from each of three strains. Strains included in the study were the ‘G3-multiplier’ released to hatcheries, a ‘control’ (putatively genetically equivalent to the unimproved base population which was spawned from fish of river origin) and fish sourced from a ‘commercial’ hatchery. Once stocked, fish were managed according to each farmer’s normal practices.ResultsThe G3-multiplier was found to be the most rapidly growing strain. Back-transformed means for harvest weight across farms for the commercial, control and G3-multiplier strains were 594 g, 659 g and 914 g, respectively, in Jashore, and 545 g, 626 g and 845 g in Natore–Rajshahi.DiscussionThese results equate to realised genetic gains of 38.6% (Jashore) and 34.9% (Natore–Rajshahi) for the G3-multiplier over the control strain and provide evidence that a family-based (i.e. pedigree-based) approach to genetic improvement is able to generate substantial levels of genetic gain in rohu. Furthermore, the clear growth advantages exhibited by the G3-multiplier strain over the control and commercial strains in this study, should encourage more Bangladeshi hatcheries, nurseries and farmers to adopt genetically improved rohu.

Weighted kernels improve multi-environment genomic prediction

Crucial to variety improvement programs is the reliable and accurate prediction of genotype’s performance across environments. However, due to the impactful presence of genotype by environment (G×E) interaction that dictates how changes in expression and function of genes influence target traits in different environments, prediction performance of genomic selection (GS) using single-environment models often falls short. Furthermore, despite the successes of genome-wide association studies (GWAS), the genetic insights derived from genome-to-phenome mapping have not yet been incorporated in predictive analytics, making GS models that use Gaussian kernel primarily an estimator of genomic similarity, instead of the underlying genetics characteristics of the populations. Here, we developed a GS framework that, in addition to capturing the overall genomic relationship, can capitalize on the signal of genetic associations of the phenotypic variation as well as the genetic characteristics of the populations. The capacity of predicting the performance of populations across environments was demonstrated by an overall gain in predictability up to 31% for the winter wheat DH population. Compared to Gaussian kernels, we showed that our multi-environment weighted kernels could better leverage the significance of genetic associations and yielded a marked improvement of 4–33% in prediction accuracy for half-sib families. Furthermore, the flexibility incorporated in our Bayesian implementation provides the generalizable capacity required for predicting multiple highly genetic heterogeneous populations across environments, allowing reliable GS for genetic improvement programs that have no access to genetically uniform material.

The Changes in Seed Germination Capacity, Seedling Growth, and Leaf Morphology of Ficus variegata Blume Influenced by Gamma-Ray Irradiation

Gamma irradiation treatments have commonly been applied to induce variation in plant genetic improvement programs. The improvement of nyawai (Ficus variegata Blume) is urgently needed mainly to break the seed dormancy, increase seedling growth, and induce variation for selecting desired traits. This research aimed to assess the effect of gamma irradiation doses on seed germination, seedling growth, and leaf morphology of Ficus variegate Blume. This experiment's irradiation doses ranged from 5-240 Gy and were applied to seeds with varying levels of vigor based on the artificial seed aging process. The data displayed a positive relationship between low doses of gamma irradiation and the nyawai seed's endurance. Low irradiation doses, 5 to 30 Gy, are deemed capable of promoting seedling development, leaf retention, and diversity in leaf structure. The higher irradiation doses than 30 Gy decreased seedling growth, leaf number, and seedling survival. In addition, these doses also affect some morphological changes, including seedling height and leaf length and width.

Viabilidade da visão computacional no melhoramento genético na produção de raízes de batata-doce

ABSTRACT The improvement of sweet potato is a costly job due to the large number of characteristics to be analyzed for the selection of the best genotypes, making it necessary to adopt new technologies, such as the use of images, associated with the phenotyping process. The objective of this research was to develop a methodology for the phenotyping of the root production aiming genetic improvement of half-sib sweet potato progenies through computational analysis of images and to compare its performance to the traditional methodology of evaluation. Sixteen half-sib sweet potato families in a randomized block design with 4 replications were evaluated. At plant level, the weight per root and the total number of roots were evaluated. The images were acquired in a “studio” made of mdf with a digital camera model Canon PowerShotSX400 IS, under artificial lighting. The evaluations were carried out using the R software, where a second-degree polynomial regression model was fitted to predict the root weight (in grams) and the genetic values and expected gains were obtained. It was possible to predict the root weight at plant and plot level, obtaining high coefficients of determination between the predicted and observed weight. Computer vision allowed the prediction of root weight, maintaining the genotype ranking and consequently the similarity between the expected gains with the selection. Thus, the use of images is an efficient tool for sweet potato genetic improvement programs, assisting in the crop phenotyping process.

Genetic diversity and structure of an active germplasm collection of Annona squamosa L.

The fruits of Annona squamosa L. are highly appreciated for their sweet taste and their nutritional and medicinal properties. Since the species is threatened by habitat loss, germplasm conservation is of the utmost importance. The present study aimed to characterize genetic variability among 19 accessions of A. squamosa maintained in the Active Germplasm Bank (AGB) of Embrapa Meio-Norte, Teresina, Piauí, Brazil, and to determine whether the geographical distribution of the genotypes influenced population structure. The accessions were derived from populations originally located in orchards situated some 200 km apart in three municipalities in the northeast of Brazil, namely Timon, Bom Jesus and Canto do Buriti. Leaf DNA was extracted and analyzed by inter simple sequence repeat (ISSR)-polymerase chain reaction. Nine ISSR primers generated 127 scorable bands of which 101 (79.52%) were polymorphic. The within-population diversity was high (Canto do Buriti), intermediary (Timon) and low (Bom Jesus). Unweighted pair-group method with arithmetic averages and Bayesian analysis of polymorphic bands separated the genotypes into two main clusters according to genetic distance and ancestry (vegetative- and seed-propagated groups), indicating that the geographical location of the populations did not influence the genetic diversity of the accessions. While ISSR marker-based DNA fingerprinting of the 19 studied accessions revealed a degree of genetic diversity between populations, the variability detected within each population was somewhat higher. This information will contribute to a better understanding of genetic variation and population structure of the accessions of A. squamosa in the AGB of Embrapa Meio-Norte, and provide crucial information for future conservation and genetic improvement programs of the species.