Recurrent Selection Research Articles

Genotyping marker density and prediction models effects in long-term breeding schemes of cross-pollinated crops.

In genomic recurrent selection, the more markers, the better because they buffer the linkage disequilibrium losses caused by recombination over cycles, and consequently, provide higher responses to selection. Reductions of genotyping marker density have been extensively evaluated as potential strategies to reduce the genotyping costs of genomic selection (GS). Low-density marker panels are appealing in GS because they entail lower multicollinearity and computing time and allow more individuals to be genotyped for the same cost. However, statistical models used in GS are usually evaluated with empirical data, using "static" training sets and populations. This may be adequate for making predictions during a breeding program's initial cycles but not for the long-term. Moreover, studies that focus on long selective breeding cycles generally do not consider GS models with the effect of dominance, which is particularly important for breeding outcomes in cross-pollinated crops. Hence, dominance effects are important and unexplored in GS for long-term programs involving allogamous species. To address it, we employed two approaches: analysis of empirical maize datasets and simulations of long-term breeding applying phenotypic and genomic recurrent selection (intrapopulation and reciprocal schemes). In both schemes, we simulated twenty breeding cycles and assessed the effect of marker density reduction on the population mean, the best crosses, additive variance, selective accuracy, and response to selection with models [additive, additive-dominant, general (GCA), and this plus specific combining ability (GCA + SCA)]. Our results indicate that marker reduction based on linkage disequilibrium levels provides useful predictions only within a cycle, as accuracy significantly decreases over cycles. In the long-term, without training set updating, high-marker density provides the best responses to selection. The model to be used depends on the breeding scheme: additive for intrapopulation and additive-dominant or GCA + SCA for reciprocal.

Registration of ‘Sims’ little bluestem

Abstract‘Sims’ (Reg. no. CV‐17, PI 700041) little bluestem [Schizachyrium scoparium (Michx.) Nash] was selected for greater 7‐d laboratory seed germination and superior field emergence. Two cycles of recurrent selection were used to develop Sims from little bluestem germplasm UC‐2 (PI 676265). Cycle 1 consisted of germinating 3,500 open‐pollinated pure seed (spikelets) of germplasm UC‐2 (designated UC‐2 C0) in water of –0.8 MPa potential for 7 d. All seed that germinated in 7 d were selected to create population UC‐2 C1. Cycle 2 selection was identical to Cycle 1 selection except that population UC‐2 C1 was used to create population UC‐2 C2 = Sims. The 7‐d seed germination of Sims in deionized water averaged 68% compared with 39, 53, and 71 for ‘Cimarron’, ‘Aldous’, and ‘Ahring’, respectively. Sixty days after field planting, plant population density of Sims averaged 8.9 plants m−2 compared with 7.1, 8.4, and 9.4 plants m−2 for Aldous, Cimarron, and Ahring, respectively. Thus, recurrent selection for increased seed germination in a negative water potential resulted in a little bluestem population capable of rapid seed germination and field emergence. Sims little bluestem is useful for livestock grazing, wildlife habitat, soil and water conservation, renewable energy, and horticultural landscapes in the U.S. southern Great Plains. Sims was released cooperatively by the USDA‐ARS and USDA‐NRCS.

Germination and field establishment of Indiangrass populations selected for greater laboratory seed germination in a simulated dry condition

Germination and field establishment of Indiangrass populations selected for greater laboratory seed germination in a simulated dry condition

Recurrent selection of new breeding lines and yield potential, nutrient profile and in vitro rumen characteristics of Melilotus officinalis

Melilotus officinalis is an important forage and green manure crop. There is a high degree of genetic diversity within species of M. officinalis . Despite the forage potential and the ability of nitrogen fixation, it has not been propagated in recent years because its high coumarin content. As a forage crop, the breeding goal of M. officinalis was mainly focused on improving forage yield and quality and reducing coumarin content. In this study, 25 superior half sib (HS) families of M. officinalis were used to carry out the second cycle recurrent selection, and genotypic variation of key traits (yield, quality and coumarin content) at two locations during 2018 and 2019 seasons were evaluated. Significant genotypic variation existed for the key traits: plant height (PH), dry biomass (DB), crude protein (CP), acid detergent fiber, neutral detergent fiber and coumarin. Also, significant genotype × location interactions were observed for the traits: DB, PH, CP, stem diameter, acid detergent lignin and acid insoluble ash ( P < 0.05). Coumarin was negatively correlated with DB and PH, and positively correlated with CP. Genetic gain of all the traits of the second cycle recurrent selection were lower than that of the first cycle recurrent selection, except for PH and leaf/stem ratio (LSR). After the second cycle recurrent selection, the genetic gains of coumarin and LSR were higher than for other traits. Furthermore, new breeding lines generated by polycrossing superior HS families were evaluated. The polycrossing improved the yield and in vitro rumen fermentation characteristics and reduced the coumarin content. Our work provides new breeding lines of M. officinalis, beneficial for a sustainable grassland-based livestock industry. • Genotype × environment interactions affect yield and quality traits. • Recurrent selection process is useful to obtain plant materials with low coumarin content and high yield. • Superiority of new M. officinalis lines over currently grown demonstrated on fields and in vitro rumen fermentation. • We developed new breeding lines of M. officinalis beneficial for livestock industry.

Strategies for Robusta Coffee (Coffea canephora) Improvement as a New Crop in Colombia

Robusta coffee is mostly grown in Africa and Asia and parts of tropical America, but not yet in Colombia. The crop has potential in lowland areas of this traditional Arabica coffee producer. Compared to Arabicas grown in highland areas, the Robustas have more drought and heat tolerance. However, they differ in flavor and have higher caffeine levels. With natural resistance to some of the major pests and diseases of other coffees, such as rust and berry borers, they thrive under harsh conditions. The genetic improvement of Robusta coffee requires the understanding of its genetic resources and a good breeding strategy. This review discusses the traits of interest and selection criteria for breeding and recommends methods of varietal development for Robusta in Colombia. Most of the traits of importance in breeding are quantitative and of low or intermediate heritability. Robusta is an outcrossing species and can suffer from inbreeding depression, so mass and recurrent selection are used, followed by the clonal propagation of best plants. Colombia has limited germplasm only from the Congolese group, so the SG1/Conilon and SG2 genotypes should be introduced with quarantine. Issues to address include the timing of flowering, asynchronous fruit maturation, chemical composition and sensory quality, as well as bean size. Variability for abiotic stress tolerance exists in Robusta genotypes and needs further study. New methods of breeding include hybrid development and recurrent selection. Having adapted varieties of Robusta coffee should promote production in Colombia, as it has in regions of Brazil, and would complement Arabica coffee for this traditional and major producer.

Genetics of growth and yield attributing traits of brinjal (Solanum melongena L.) through six generation mean analysis

Understanding gene action of different traits is of utmost importance for formulating successful breeding programs. The population was developed involving Arka Neelachal Shyama and CARI-1 to inquire the gene actions controlling the inheritance of several growth as well as yield attributingparameters through six-generation mean analysis. Three parameter model revealed the insufficiency of the simpler additive dominance model for the evaluated traits, referring to the existence of inter-allelic interactions. Six parameter model was implemented to better understand gene actions. Most of the yield and attributing traits under study except number of branches showed a high estimate of dominance as well as environmental variance, disclosing a lower extent of heritability. The number of branches was observed to be controlled by duplicate epistasis. Hence, for the fixation of this trait, the best strategy is to exercise minimal selection during advance generations, followed by intense selection during later generations (F4- population onwards). The preponderance of the narrow sense type of heritability revealed that dominant effects were predominantly accountable for the existing genetic variation. Hence, recurrent selection followed by bi-parental mating and selection during the later stage of generations is advised to increase the occurrence of favorable alleles and accumulation of desirable genes.

Inheritance of traits related to yield and fatty acid profile of winter squash seed oil

The objective of this study was to determine the inheritance of traits related to seed oil yield and fatty acid profile components and to estimate the genetic relationships between these traits in Cucurbita moschata D. This study assessed six generations derived from crosses between parents with contrasting traits under study. F1 plants were obtained from the crossing between BGH 7319 (P1) and ‘Tronco Verde’ (P2), which were subsequently self-fertilized to obtain the F2 generation. F1 plants were also backcrossed with the P1 and P2 parents to obtain the BC1 and BC2 generations, respectively. In general, additive effects were predominant for most of the traits, and thus, the development of inbred lines is the recommended strategy for genetic improvement of these traits. Dominance effects were significant even under low expression. This demonstrates that the performance of progeny tests throughout the selfing generations will enable the distinction between genotypes, thus providing greater efficiency in selection and, consequently, greater genetic gains. In addition, overdominance was observed in oil content; therefore, the development of hybrids with genotypes causing high oil content is attainable. In general, the estimates of genetic correlations had a high magnitude and were favorable to the increase in functional oil productivity, associated with better quality of fatty acid profiles. Recurrent intrapopulation selection aimed at the development of open-pollinated varieties with high productivity, associated with greater stability of the functional oil in C. moschata, may be useful.

Conservation and Convergence of Genetic Architecture in the Adaptive Radiation of Anolis Lizards.

AbstractThe G matrix, which quantifies the genetic architecture of traits, is often viewed as an evolutionary constraint. However, G can evolve in response to selection and may also be viewed as a product of adaptive evolution. Convergent evolution of G in similar environments would suggest that G evolves adaptively, but it is difficult to disentangle such effects from phylogeny. Here, we use the adaptive radiation of Anolis lizards to ask whether convergence of G accompanies the repeated evolution of habitat specialists, or ecomorphs, across the Greater Antilles. We measured G in seven species representing three ecomorphs (trunk-crown, trunk-ground, and grass-bush). We found that the overall structure of G does not converge. Instead, the structure of G is well conserved and displays a phylogenetic signal consistent with Brownian motion. However, several elements of G showed signatures of convergence, indicating that some aspects of genetic architecture have been shaped by selection. Most notably, genetic correlations between limb traits and body traits were weaker in long-legged trunk-ground species, suggesting effects of recurrent selection on limb length. Our results demonstrate that common selection pressures may have subtle but consistent effects on the evolution of G, even as its overall structure remains conserved.

Strategies for the recurrent selection program in tobacco breeding for green leaf yield

In conducting a recurrent selection (RS) program in tobacco (Nicotiana tabacum L.), inbred and noninbred progenies as well as double-haploid (DH) progenies can be used. There is also the possibility of recombining the selected progenies using half-sib (HS) or full-sib (FS) progenies. To choose the best RS strategy, the breeder's equation can be used. When using inbred progenies with an allelic frequency other than 50%, one of the genetic variance components is the genetic covariance between additive effects and homozygous dominance effects (D1). This component may present negative values and is part of the numerator in the equation for gain from selection (GS). Thus, the objective of this study was to estimate the genetic variance components in a tobacco population and compare the different strategies to conduct RS. From an RS population, HS, FS, and S1:2 inbred progenies were evaluated in different experiments. The dominance variance was null. In this condition, the estimate of D1 is not significant, meaning that D1 does not influence the GS in the RS program. With the obtained estimates, the GS was estimated for the seven different strategies for conducting the RS program. The use of DH lines in tobacco RS represents the best strategy. Other strategies allow expressive GS, such as the alternate use of inbred and FS progenies, for evaluation and FS progenies for recombination.

Genetic gains in Passiflora for resistance to cowpea aphid-borne mosaic virus using recurrent selection

Genetic gains in Passiflora for resistance to cowpea aphid-borne mosaic virus using recurrent selection

Additive and Non-Additive Effects on the Control of Key Agronomic Traits in Popcorn Lines under Contrasting Phosphorus Conditions.

Phosphorus is a non-renewable natural resource that will run out of reserves in the upcoming decades, making it essential to understanding the inheritance of nutrient use efficiency for selecting superior genotypes. This study investigated the additive and non-additive effects of commercially relevant traits for the popcorn crop (grain yield—GY, popping expansion—PE, and expanded popcorn volume per hectare—PV) in different conditions of phosphorus (P) availability in two locations in Rio de Janeiro State, Brazil. Six S7 lines previously selected for P use—L59, L70, and P7, efficient and responsive; and L54, L75, and L80, inefficient and non-responsive—were used as testers in crosses with 15 progenies from the fifth cycle of intrapopulation recurrent selection of UENF-14, with adaptation to the North and Northwest regions of Rio de Janeiro State. Using the Griffing diallel analysis, P use efficiency was predominantly additive in the expression of PE, and non-additive effects were prominent for GY and PV. For obtaining genotypes that are efficient for phosphorus use, it is recommended that heterosis with parents that provide additive gene accumulation for PE be explored.

ImpMKT: the imputed McDonald and Kreitman test, a straightforward correction that significantly increases the evidence of positive selection of the McDonald and Kreitman test at the gene level.

The McDonald and Kreitman test is one of the most powerful and widely used methods to detect and quantify recurrent natural selection in DNA sequence data. One of its main limitations is the underestimation of positive selection due to the presence of slightly deleterious variants segregating at low frequencies. Although several approaches have been developed to overcome this limitation, most of them work on gene pooled analyses. Here, we present the imputed McDonald and Kreitman test (impMKT), a new straightforward approach for the detection of positive selection and other selection components of the distribution of fitness effects at the gene level. We compare imputed McDonald and Kreitman test with other widely used McDonald and Kreitman test approaches considering both simulated and empirical data. By applying imputed McDonald and Kreitman test to humans and Drosophila data at the gene level, we substantially increase the statistical evidence of positive selection with respect to previous approaches (e.g. by 50% and 157% compared with the McDonald and Kreitman test in Drosophila and humans, respectively). Finally, we review the minimum number of genes required to obtain a reliable estimation of the proportion of adaptive substitution (α) in gene pooled analyses by using the imputed McDonald and Kreitman test compared with other McDonald and Kreitman test implementations. Because of its simplicity and increased power to detect recurrent positive selection on genes, we propose the imputed McDonald and Kreitman test as the first straightforward approach for testing specific evolutionary hypotheses at the gene level. The software implementation and population genomics data are available at the web-server imkt.uab.cat.

Study of gene action in different traits of maize (Zea mays L.)

A study was conducted on maize incorporating a total of 28 single crosses, eight parental lines and two standard checks to determine the combining ability and gene action. Among the eleven traits that were studied, the analysis of variance revealed that the mean squares due to genotypes, parents and hybrids were highly significant for all traits, except for 100 grain weight in case of parents, indicating the presence of an adequate amount of genetic variability. Onfurther analysis of variance for combining ability,the mean squares due to GCA and SCA were observed to be highly significant for almost all traits indicating the role of both additive and non additive components of genetic variance in the expression of all the studied traits.The &nbsp;high gca effect for grain yield per plant was associated with high or average gcafor yield component traits for most parents, while the poor combiners for grain yield per plant were also poor combiners for other yield component traits.High sca effects were seen in a few cross combinations which were good specific combiners for grain yield per plant and yield component traits.Based on the gca effects some inbred lines were identified as good general combiners for various traits. This indicated that these parents could be utilized for developing synthetic variety.The inbred lines with desirable gca effects for grain yield and other agro-morphological traits could be inter-crossed to develop an improved base population and subsequent recurrent selection efforts would facilitate the derivation of elite lines excelling in desirable character.All ofthe cross combinations exhibiting desirable significant sca effect were having one parent as a good or average combiner for each of the eleven agro morphological traits studied.It was clear that these hybrids were the combinations of either &nbsp;the parents as good general combiners or one of the parents as a good general combiner for yield and yield related traits. Hence, they can be used as a potential single cross hybrid combination and tested further.The crosses that show high sca effects indicate a preponderance of non-additive genes and can be used for heterosis breeding. Keywords: Maize, Combining ability, GCA and SCA

Screening and Validation of SSR Molecular Markers for Identification of Downy Mildew Resistance in Intraspecific Hybrid F1 Progeny (V. vinifera)

Downy mildew is a major disease that severely restricts the healthy and sustainable development of the global grape and wine industry, so there is significant interest in breeding high-quality disease-resistant varieties. In this study, hybridization was carried out between two disease-resistant and four high-quality varieties for eight hybrid combinations. The downy mildew resistance of 6 hybrid parents and 350 hybrid F1 progeny was determined by the leaf disc inoculation test, and the frequency distribution of the disease resistance grades was analyzed for the different populations. Agarose gel electrophoresis and disease resistance identification were used to screen SSR molecular markers of the tested hybrids for resistance to downy mildew. The results showed that minor disease-resistance genes in V. vinifera varieties were the main determinant of the variation in disease susceptibility among different varieties. V. vinifera resistance to downy mildew is inherited by a quantitative trait controlled by multiple genes. Intraspecific hybridization of V. vinifera can be applied to breed suitable intermediate materials or new types of disease resistance. The screening and verification of simple-sequence repeats (SSR) as molecular markers revealed that UDV-304, UDV-305, and UDV-737 could be used as standard markers for the identification of downy mildew resistance of hybrid progeny of Ecolly and Cabernet Sauvignon, UDV-305 could be used for the hybrid progeny of Meili and Cabernet Sauvignon, and VMC8g9 could be used for the hybrid progeny of Ecolly or Meili and Dunkelfelder. The disease-resistant progeny selected in this study can be used as intermediate materials for the breeding of new high-quality, disease-resistant varieties by intraspecific recurrent selection in V. vinifera. The screened standard markers can be utilized for rapid batch identification of hybrid progeny of different hybrid combinations to facilitate molecular marker-assisted breeding.

Recurrent haploid selection in a population of sweet corn (Zea mays convar. saccharata)

AbstractRecurrent haploid selection is based on the phenotype of haploid plants. This selection method was reported to be very effective because of the high selection pressure. The aim of this study was to quantify the effect of five generations of recurrent haploid selection on a sweet corn population developed by intercrossing 40 hybrid cultivars. We compared the initial population, five cycles of recurrent haploid selection, and mass selection after five cycles in six environments. The results indicated that recurrent haploid selection had no positive effect on yield or quality. For the traits tillering, tip fill, total yield and total number of ears, significant changes from cycle to cycle were observed but in differing directions. The performance per se of single haploid plants has probably a low correlation to their combining ability in a population. Positive mass selection of the best ears resulted in no improvement of total yield, a reduction of marketable yield and about 2‐day delay of flowering. In conclusion, recurrent haploid selection based on the phenotype of individual plants was not an efficient method to improve the sweet corn population investigated.

Blue revolution for food security under carbon neutrality: A case from the water-saving and drought-resistance rice

Blue revolution for food security under carbon neutrality: A case from the water-saving and drought-resistance rice

Evidence of recurrent selection of mutations commonly found in SARS-CoV-2 variants of concern in viruses infecting immunocompromised patients.

Chronically immunosuppressed patients infected with SARS-CoV-2 often experience prolonged virus shedding, and may pave the way to the emergence of mutations that render viral variants of concern (VOC) able to escape immune responses induced by natural infection or by vaccination. We report herein a SARS-CoV-2+ cancer patient from the beginning of the COVID-19 pandemic whose virus quasispecies across multiple timepoints carried several immune escape mutations found in more contemporary VOC, such as alpha, delta and omicron, that appeared to be selected for during infection. We hypothesize that immunosuppressed patients may represent the source of VOC seen throughout the COVID-19 pandemics.

Inheritance studies through generation mean analysis for quantitative traits in soybean (Glycine max (L.) Merrill.)

Most of the economically important traits in soybean are quantitatively inherited. The generation mean analysis involving a five-parameter model was carried out in four crosses, viz., Pratap Soya- 2 × LP 5-2, Co 3 × LP 5-2, Co 3 × LP 5-1 and Co 3 × LP 13-1 to investigate additive, dominance and epistatic variance. Therefore, F1, F2 and F3 generations of the above four crosses were evaluated along with their respective parents to estimate the gene action for eleven quantitative traits through generation mean analysis, which provides information about all the gene interactions. The crosses Co 3 × LP 5-1 and Co 3 × LP 13-1 for plant height, Pratap Soya-2 × LP 5-2 for protein content and Co 3 × LP 5-2 for both oil content and seed yield per plant exhibited the adequacy of the additive dominance model. The remaining crosses exhibited epistatic interactions with all other traits. Hence simple recurrent selection can be followed to increase the frequency of desirable genes in the population and the resulted improved population can be used to develop superior lines with desirable genes by pedigree breeding. The crosses Co 3 × LP 5-1 and Pratap Soya - 2 × LP 5-2 were best for further selection programmes with regard to seed yield and quality improvement.

Genomic prediction for canopy height and dry matter yield in alfalfa using family bulks.

Genomic selection (GS) has proven to be an effective method to increase genetic gain rates and accelerate breeding cycles in many crop species. However, its implementation requires large investments to phenotype of the training population and for routine genotyping. Alfalfa (Medicago sativa L.) is one of the major cultivated forage legumes, showing high-quality nutritional value. Alfalfa breeding is usually carried out by phenotypic recurrent selection and is commonly done at the family level. The application of GS in alfalfa could be simplified and less costly by genotyping and phenotyping families in bulks. For this study, an alfalfa reference population composed of 142 full-sib and 35 half-sib families was bulk-genotyped using target enrichment sequencing and phenotyped for dry matter yield (DMY) and canopy height (CH) in Florida, USA. Genotyping of the family bulks with 17,707 targeted probes resulted in 114,945 single-nucleotide polymorphisms. The markers revealed a population structure that matched the mating design, and the linkage disequilibrium slowly decayed in this breeding population. After exploring multiple prediction scenarios, a strategy was proposed including data from multiple harvests and accounting for the G×E in the training population, which led to a higher predictive ability of up to 38 and 24% for DMY and CH, respectively. Although this study focused on the implementation of GS in alfalfa families, the bulk methodology and the prediction schemes used herein could guide future studies in alfalfa and other crops bred in bulks.

Inheritance of fruit colour, fruit ridge pattern and related traits through generation mean analysis in bitter gourd (Momordica charantia L.)

Analysis of generation means in P1, P2, F1, F2, B1 and B2generations of two bitter gourd crosses viz., IIHR Sel-5-8 ×IIHR-144-1 and Arka Harit × IIHR-144-1 were performed todetermine the nature of gene action governing fruit traits.All the parents and generations differed significantly forthe observed traits. For the cross IIHR Sel-5-8 × IIHR-144-1,Chi-square tests in the segregating generations for fruitcolour and fruit ridge pattern were fitted well with theMendelian phenotypic ratio of 3:1. This indicates that greenfruit colour of bitter gourd is governed by single dominantgene and is dominant over white fruit colour. Fruit ridgepattern indicated that the discontinuous ridge of bitter gourdis also governed by monogenic dominant gene and isdominant over continuous ridge. All the quantitative traitsstudied (peduncle length, fruit length and fruit girth) showednon-allelic gene interaction in both the crosses indicatingpresence of epistatic gene action. Nature of gene actionvaried with the character and among crosses and bothadditive and non-additive gene action was involved inexpression of the characters having the duplicate epistasis.This indicates use of reciprocal recurrent selection forimprovement of these traits and also the possibilities ofarriving at better transgressive segregants by selfing thehybrids developed using such selected materials.