An Introduction to Some Concepts in Statistical Analysis and Quantitative Genetics for Sugarcane Breeding Programs

Sugar Tech ◽  
2021 ◽  
Author(s):  
Phillip Jackson ◽  
Emily Deomano ◽  
Xianming Wei
Keyword(s):  
Statistical Analysis ◽  
Quantitative Genetics ◽  
Breeding Programs ◽  
Sugarcane Breeding

scholarly journals Applications of Quantitative Genetics and Statistical Analyses in Sugarcane Breeding

Sugar Tech ◽  
2021 ◽  
Author(s):  
Jean-Yves Hoarau ◽  
Thomas Dumont ◽  
Xianming Wei ◽  
Philip Jackson ◽  
Angélique D’Hont
Keyword(s):  
Quantitative Genetics ◽  
New Technologies ◽  
Statistical Analyses ◽  
Development Programs ◽  
Breeding Programs ◽  
Sugarcane Breeding ◽  
Breeding Research ◽  
Term Basis ◽  
New Varieties ◽  
High Yielding Varieties

AbstractSugarcane breeding programs aim to deliver new high-yielding varieties, resistant to diseases and pests, which contribute to profitability and sustainability of cane industries. These programs generally mobilize significant experimental, technological and human resources on long-term basis. Their efficiency in terms of genetic gains per unit of cost and time and their ability to release new varieties rely on the development of many breeding applications based on quantitative genetics theory and on statistical analyses of numerous experimental data from selection schemes including DNA marker data developed for some genomic breeding applications. New methodological approaches and new technologies that might better guide and support breeding research in cultivars development programs are continually sought. This paper presents an overview of the main applications developed in statistical methodology in support of the efficiency of sugarcane breeding programs. For each type of application, its conceptual and methodological framework is presented. Implementation issues are reviewed as well as the main scientific and practical achievements so far obtained.

scholarly journals Population Genomics Along With Quantitative Genetics Provides a More Efficient Valorization of Crop Plant Genetic Diversity in Breeding and Pre-breeding Programs

2021 ◽  
Author(s):  
Peter Civan ◽  
Renaud Rincent ◽  
Alice Danguy-Des-Deserts ◽  
Jean-Michel Elsen ◽  
Sophie Bouchet
Keyword(s):  
Genetic Diversity ◽  
Quantitative Genetics ◽  
Genetic Gain ◽  
Recurrent Selection ◽  
Prediction Models ◽  
Population Genomics ◽  
Breeding Program ◽  
Breeding Programs ◽  
Sequencing Technologies ◽  
Genetic Value

AbstractThe breeding efforts of the twentieth century contributed to large increases in yield but selection may have increased vulnerability to environmental perturbations. In that context, there is a growing demand for methodology to re-introduce useful variation into cultivated germplasm. Such efforts can focus on the introduction of specific traits monitored through diagnostic molecular markers identified by QTL/association mapping or selection signature screening. A combined approach is to increase the global diversity of a crop without targeting any particular trait.A considerable portion of the genetic diversity is conserved in genebanks. However, benefits of genetic resources (GRs) in terms of favorable alleles have to be weighed against unfavorable traits being introduced along. In order to facilitate utilization of GR, core collections are being identified and progressively characterized at the phenotypic and genomic levels. High-throughput genotyping and sequencing technologies allow to build prediction models that can estimate the genetic value of an entire genotyped collection. In a pre-breeding program, predictions can accelerate recurrent selection using rapid cycles in greenhouses by skipping some phenotyping steps. In a breeding program, reduced phenotyping characterization allows to increase the number of tested parents and crosses (and global genetic variance) for a fixed budget. Finally, the whole cross design can be optimized using progeny variance predictions to maximize short-term genetic gain or long-term genetic gain by constraining a minimum level of diversity in the germplasm. There is also a potential to further increase the accuracy of genomic predictions by taking into account genotype by environment interactions, integrating additional layers of omics and environmental information.Here, we aim to review some relevant concepts in population genomics together with recent advances in quantitative genetics in order to discuss how the combination of both disciplines can facilitate the use of genetic diversity in plant (pre) breeding programs.

scholarly journals Productive capacity and genetic variation behavior in progenies from irrigated açai according to plant age

2020 ◽  
Vol 14 ◽  
Author(s):  
João Tomé de Farias Neto ◽  
Gilberto Ken Iti Yokomizo ◽  
Marcos Deon Vilela de Resende
Keyword(s):  
Genetic Variation ◽  
Statistical Analysis ◽  
Block Design ◽  
Fruit Yield ◽  
Plant Age ◽  
Productive Capacity ◽  
Breeding Programs ◽  
Production Chain ◽  
Randomized Block Design ◽  
Adult Plants

The açai fruit yield is concentrated between the months of July to December (harvest), providing an important income to actors involved in the production chain, however in the off-season this brings serious socioeconomic problems, with the need for research that may offer selected genetic materials that can circumvent this problem. However, the age for making this selection in this species is unknown. Therefore, the objective of this work was to infer the best age for selection by estimating genetic and phenotypic parameters in the different stages of evaluating progenies of half-sibs of acai. The experiment followed a randomized block design with three replications and five plants per plot, with 30 progenies. The statistical analysis was performed using the REML/BLUP methodology. The results showed that the magnitudes of the estimates of heritability and genetic variation decrease with age; the correlations between the characters that make up fruit yield reveal that the number of bunches is the most important component of yield; for the fruit yield character, the age of progenies and harvest years indicate that early selections are more efficient; the early emission of tillers is an important characteristic to be sought in açai breeding programs guaranteeing greater fruit yield in adult plants; and higher fruit yield in the off-season is possible from the fourth year of harvest.

scholarly journals Historical Use of Cultivars as Parents in Florida and Louisiana Sugarcane Breeding Programs

2015 ◽  
Vol 2015 ◽  
pp. 1-9 ◽  
Author(s):  
James Todd ◽  
Barry Glaz ◽  
David Burner ◽  
Collins Kimbeng
Keyword(s):  
Genetic Diversity ◽  
State University ◽  
Breeding Programs ◽  
Abiotic And Biotic Stresses ◽  
Biotic Stresses ◽  
Sugarcane Breeding ◽  
Louisiana State University ◽  
Loss Of Diversity ◽  
High Diversity

Sugarcane (Saccharum L. spp. hybrids) growers depend on breeding programs for new, high-yielding cultivars that have resistance to abiotic and biotic stresses, so breeders continually seek out widely adapted, high yielding germplasm to be used as parents for their programs. Cultivars are sometimes used for this purpose, but their use may be minimized to prevent genetic diversity erosion. The purpose of this study was to determine the importance of cultivars as parents in three USA (one in Florida and two in Louisiana) sugarcane breeding programs by quantifying the percentage of cultivars that had these parental groupings based on published registrations and crossing records. The percentage of cultivars with at least one commercial parent for each program was 81.8%, 77.5%, and 64.3% for the Houma (Ho), Louisiana, Canal Point (CP), Florida and Louisiana State University (LSU) programs, respectively, but cultivars were recently used as parents in only 11.8% (Ho), 16.39% (CP), and 34.3% (LSU) of crosses. The results indicate that the CP and Ho programs should consider increasing the use of cultivars as parents in their breeding programs to increase the probability of selecting potential commercial genotypes, but this should be balanced with high diversity crosses to avoid the loss of diversity.

scholarly journals Predicting the future of plant breeding: complementing empirical evaluation with genetic prediction

2014 ◽  
Vol 65 (4) ◽  
pp. 311 ◽  
Author(s):  
Mark Cooper ◽  
Carlos D. Messina ◽  
Dean Podlich ◽  
L. Radu Totir ◽  
Andrew Baumgarten ◽  
...  
Keyword(s):  
Plant Breeding ◽  
Quantitative Genetics ◽  
Empirical Evaluation ◽  
Practical Application ◽  
Maize Breeding ◽  
Breeding Programs ◽  
Development Models ◽  
Private And Public ◽  
Germplasm Diversity

For the foreseeable future, plant breeding methodology will continue to unfold as a practical application of the scaling of quantitative biology. These efforts to increase the effective scale of breeding programs will focus on the immediate and long-term needs of society. The foundations of the quantitative dimension will be integration of quantitative genetics, statistics, gene-to-phenotype knowledge of traits embedded within crop growth and development models. The integration will be enabled by advances in quantitative genetics methodology and computer simulation. The foundations of the biology dimension will be integrated experimental and functional gene-to-phenotype modelling approaches that advance our understanding of functional germplasm diversity, and gene-to-phenotype trait relationships for the native and transgenic variation utilised in agricultural crops. The trait genetic knowledge created will span scales of biology, extending from molecular genetics to multi-trait phenotypes embedded within evolving genotype–environment systems. The outcomes sought and successes achieved by plant breeding will be measured in terms of sustainable improvements in agricultural production of food, feed, fibre, biofuels and other desirable plant products that meet the needs of society. In this review, examples will be drawn primarily from our experience gained through commercial maize breeding. Implications for other crops, in both the private and public sectors, will be discussed.

Early stage selection for commercial cane sugar (CCS) in sugarcane clones: effects of time of sampling and irrigation

2003 ◽  
Vol 54 (4) ◽  
pp. 389 ◽  
Author(s):  
Phillip A. Jackson ◽  
Terry E. Morgan
Keyword(s):  
Field Experiments ◽  
Clonal Selection ◽  
Early Stage ◽  
Sugar Content ◽  
Selection Criterion ◽  
Cane Yield ◽  
Physiological Basis ◽  
Breeding Programs ◽  
Sugarcane Breeding ◽  
Selection For

Commercially recoverable sugar content in sugarcane (CCS, expressed as a percentage) is a key selection criterion in sugarcane breeding programs. In some sugarcane breeding programs there may be significant operational advantages in measuring CCS early in the crop growth cycle, well before commercial harvesting would normally commence, and in restricting growth by withholding irrigation to reduce cane yield and lodging. Two field experiments were conducted to investigate these effects. The experiments included clones representative of genotypes routinely assessed in the earliest stages of clonal selection in breeding programs. Differences among genotypes for CCS were expressed early when cane had very low CCS (in February or March), and then rates of increase in CCS following that time were similar in most genotypes. Therefore, time of sampling had little effect on ranking of genotypes for CCS, and selection for high CCS could be effective early in the year. Irrigation regime also had little effect on ranking of the clones for CCS, indicating that mild water stress could be imposed with no adverse effect on selection results. The results are discussed in relation to optimising selection procedures and systems in early stage selection trials in sugarcane breeding programs, and better understanding the physiological basis of genetic variation in CCS.

Genotype × environment interactions in sugarcane. II. Use of performance in plant cane as an indirect selection criterion for performance in ratoon crops

1992 ◽  
Vol 43 (7) ◽  
pp. 1461 ◽  
Author(s):  
PA Jackson
Keyword(s):  
Genetic Correlations ◽  
Selection Criterion ◽  
Relative Yield ◽  
Indirect Selection ◽  
Sugar Yield ◽  
Ratoon Crop ◽  
Breeding Programs ◽  
Sugarcane Breeding ◽  
Efficiency Of Selection ◽  
Plant Crop

This study aimed to determine whether sugar yield of sugarcane genotypes in the plant crop could be used to predict relative yield in subsequent ratoon crops. Results from two series of trials, planted in 1985 and 1986, were examined. Within each series genotypes were planted at four locations and evaluated in plant, first ratoon and second ratoon crops. The genotypes used had not been selected previously in the test environments. Genetic correlations between sugar yield in plant and ratoon crop-years were moderate to high (greater than 0.65) for most locations. The relative efficiency of selection for yield in ratoon crop-years via indirect selection in the plant crop-year averaged 0.67. Realized gains from selection were compared for selection based on only plant crop results and selection based on average performance across all crop-years (the latter being the method routinely used in sugarcane breeding programs at present). In most cases the increases in realized gains in yield across independent environments brought about by considering results from more than the plant crop-year were small or non-existent. In the two series of trials, 11 and 12 of the top ranking 15 genotypes, respectively, based on mean performance across all crop-years, were also in the top 15 genotypes based on only the plant crop results. It is suggested that the testing of genotypes in only the plant crop may be appropriate in the early stages of selection in sugarcane breeding programs. Resources otherwise allocated to testing early stage material in ratoon crops may be more usefully employed elsewhere such as testing in more sites, with more replicates or more genotypes. It is emphasized, however, that this strategy may not be appropriate for highly selected populations, such as those in the final stages of selection, where genetic variance and genetic correlations between crop-years would be expected to be smaller than those obtained in this study.

scholarly journals Sugarcane Breeding in Reunion: Challenges, Achievements and Future Prospects

Sugar Tech ◽  
2021 ◽  
Author(s):  
Thomas Dumont ◽  
Laurent Barau ◽  
Audrey Thong-Chane ◽  
Jordan Dijoux ◽  
Mathilde Mellin ◽  
...  
Keyword(s):  
Breeding Program ◽  
Large Network ◽  
Genetic Progress ◽  
Breeding Programs ◽  
Selection Scheme ◽  
Sugarcane Breeding ◽  
Genetics Research ◽  
Research Activities ◽  
Production Areas ◽  
Genetic Context

AbstractAll over the world, sugarcane breeding programs are developing new, high-yielding cultivars that are resistant to major diseases to improve the profitability and sustainability of the sugar-energy industries they serve. In Reunion Island, sugarcane genetic improvement efforts began in 1929. Many challenges had to be overcome. Continuous breeding efforts have been made to develop varietal resistances to control some major diseases and are still going on today. Given the extreme agroclimatic diversity that characterizes the different production areas of the industry, it was necessary to gradually develop a large network of seven decentralized breeding programs to support genetic progress throughout the whole industry. This article provides an overview of the sugarcane breeding program of Reunion. It describes historical achievements and gives detailed information about germplasm development, variety exchanges, breeding program and selection scheme and procedures. A review is also made on applied genetics research activities supporting variety improvement. Further progress depends on the optimized functioning of the current breeding program, which has never been so largely extended in terms of target environments. The article discusses prospects of genomics breeding applications in the complex genetic context of sugarcane, which will require large multidisciplinary collaborations.

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