Linkage Mapping of Biomass Production and Composition Traits in a Miscanthus Sinensis Population

Abstract Breeding miscanthus for biomass production and composition is essential for targeting high-yielding genotypes suited to different end-uses. Our objective was to understand the genetic determinism of these traits in M. sinensis, according to different plant ages and environmental conditions. A diploid population was established in two locations according to a staggered-start design, which made the “year” effect partitioned into “age” and “growing season” effects. An integrated genetic map of 2,602 SNP markers distributed across 19 LGs, was aligned with the M. sinensis reference genome and spanned 2,770 cM. The QTL mapping was based on Best Linear Unbiased Predictions estimated across three climatic conditions and at least three ages in both locations. 260 and 283 QTL were related to biomass production and composition traits, respectively. In each location, 40%-60% were related to biomass production traits and stable across different climatic conditions and ages, and 30% to biomass composition traits. Ten to fifteen% were stable for both trait types across locations. Twelve QTL clusters were established based on either biomass production or composition traits, and validated by high genetic correlations between the traits. Sixty-two putative M. sinensis genes, related to the cell-wall, were evidenced in the QTL clusters of biomass composition traits, and orthologous to those of sorghum and maize. Twelve of them were differentially expressed and belonged to gene families related to the cell-wall biosynthesis identified in other miscanthus studies. These stable QTL constitute new insights into Marker-Assisted Selection breeding while offering a joint improvement of biomass production or composition traits.

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Estimation of Genetic Parameters of Biomass Production and Composition Traits in Miscanthus Sinensis Using a Staggered-start Design

10.21203/rs.3.rs-354838/v1 ◽

2021 ◽

Author(s):

Raphael Raverdy ◽

Emilie Mignot ◽

Stéphanie Arnoult ◽

Laura Fingar ◽

Guillaume Bodineau ◽

...

Keyword(s):

Biomass Production ◽

Genetic Parameters ◽

Genetic Variance ◽

Biomass Composition ◽

Miscanthus Sinensis ◽

Individual Plant ◽

Production Traits ◽

Genetic Progress ◽

Year Effect ◽

Large Interaction

Abstract Traits for biomass production and composition make Miscanthus a promising bioenergy crop for different bioconversion routes. They need to be considered in miscanthus breeding programs as they are subjected to genetic and genetic x environment factors. The objective was to estimate the genetic parameters of an M. sinensis population grown during four years in two French locations. In each location, the experiment was established according to a staggered-start design in order to decompose the year effect into age and climate effects. Linear Mixed Models were used to estimate genetic variance, genotype x age, genotype x climate interaction variances and residual variances. Individual plant broad-sense heritability means ranged from 0.42 to 0.62 for biomass production traits, and were more heritable than biomass composition traits with means ranging from 0.26 to 0.47. Heritability increased through time for most of the biomass production and composition traits. Low genetic variance along with large genotype x age and genotype x climate interaction variances tended to decrease the heritability of biomass production traits for young plant ages. Most of the production traits showed large interaction variances for age and climate in both locations, while biomass composition traits highlighted large interaction variances due to climate in Orléans. The genetic and phenotypic correlations between biomass production and composition traits were moderate and positive, while hemicelluloses were negatively correlated with all traits. Efficient genetic progress is achievable for miscanthus breeding when plants get older. The joint improvement of biomass production and composition traits would help provide a better response of miscanthus to selection.

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Methods of Increasing Miscanthus Biomass Yield for Biofuel Production

Energies ◽

10.3390/en14248368 ◽

2021 ◽

Vol 14 (24) ◽

pp. 8368

Author(s):

Evgeny Chupakhin ◽

Olga Babich ◽

Stanislav Sukhikh ◽

Svetlana Ivanova ◽

Ekaterina Budenkova ◽

...

Keyword(s):

Biomass Production ◽

Biofuel Production ◽

Biomass Composition ◽

Miscanthus Sinensis ◽

High Biomass ◽

Breeding Programs ◽

Bioenergy Production ◽

Industrial Enterprises ◽

Miscanthus Giganteus ◽

Miscanthus Sacchariflorus

The lignocellulosic perennial crop miscanthus, especially Miscanthus × giganteus, is particularly interesting for bioenergy production as it combines high biomass production with low environmental impact. However, there are several varieties that pose a hazard due to susceptibility to disease. This review contains links showing genotype and ecological variability of important characteristics related to yield and biomass composition of miscanthus that may be useful in plant breeding programs to increase bioenergy production. Some clones of Miscanthus × giganteus and Miscanthus sinensis are particularly interesting due to their high biomass production per hectare. Although the compositional requirements for industrial biomass have not been fully defined for the various bioenergy conversion processes, the lignin-rich species Miscanthus × giganteus and Miscanthus sacchariflorus seem to be more suitable for thermochemical conversion processes. At the same time, the species Miscanthus sinensis and some clones of Miscanthus × giganteus with low lignin content are of interest for the biochemical transformation process. The species Miscanthus sacchariflorus is suitable for various bioenergy conversion processes due to its low ash content, so this species is also interesting as a pioneer in breeding programs. Mature miscanthus crops harvested in winter are favored by industrial enterprises to improve efficiency and reduce processing costs. This study can be attributed to other monocotyledonous plants and perennial crops that can be used as feedstock for biofuels.

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High Heritabilities for Antibiotic Usage Show Potential to Breed for Disease Resistance in Finishing Pigs

Antibiotics ◽

10.3390/antibiotics10070829 ◽

2021 ◽

Vol 10 (7) ◽

pp. 829

Author(s):

Wim Gorssen ◽

Dominiek Maes ◽

Roel Meyermans ◽

Jürgen Depuydt ◽

Steven Janssens ◽

...

Keyword(s):

Pathogenic Bacteria ◽

Animal Health ◽

Molecular Genetic ◽

Genetic Correlations ◽

Genetic Selection ◽

Antibiotic Usage ◽

Finishing Pigs ◽

Production Traits ◽

Parenteral Antibiotic ◽

On Farm

The use of antimicrobials in animal production is under public debate, mainly due to the risk of transfer of resistance to pathogenic bacteria in humans. Therefore, measures have been taken during the last few decades to reduce antibiotic usage in animals, for instance, by national monitoring programmes and by improving animal health management. Although some initiatives exist in molecular genetic selection, quantitative genetic selection of animals towards decreased antibiotic usage is an underexplored area to reduce antibiotic usage. However, this strategy could yield cumulative effects. In this study, we derived new phenotypes from on-farm parenteral antibiotic records from commercially grown crossbred finishing pigs used in the progeny test of Piétrain terminal sires to investigate the heritability of antibiotics usage. Parenteral antibiotic records, production parameters and pedigree records of 2238 full-sib pens from two experimental farms in Belgium between 2014 and 2020 were analysed. Heritability estimates were moderate (18–44%) for phenotypes derived from all antibiotic treatments, and low (1–15%) for phenotypes derived from treatments against respiratory diseases only. Moreover, genetic correlations between these new phenotypes and mortality were low to moderate (0.08–0.60) and no strong adverse genetic correlations with production traits were found. The high heritabilities and favourable genetic correlations suggest these new phenotypes, derived from on-farm antibiotics records, to be promising for inclusion in future pig breeding programs to breed for a decrease in antibiotics usage.

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Corrigendum to: Consequences of genetic selection for environmental impact traits on economically important traits in dairy cows

Animal Production Science ◽

10.1071/an16592_co ◽

2018 ◽

Vol 58 (10) ◽

pp. 1966

Author(s):

Purna Kandel ◽

Sylvie Vanderick ◽

Marie-Laure Vanrobays ◽

Hélène Soyeurt ◽

Nicolas Gengler

Keyword(s):

Dairy Cows ◽

Body Condition Score ◽

Genetic Correlations ◽

Genetic Selection ◽

Selection Response ◽

Direct Selection ◽

Correlated Response ◽

Production Traits ◽

Ch4 Emissions ◽

Natural Logarithm

Methane (CH4) emission is an important environmental trait in dairy cows. Breeding aiming to mitigate CH4 emissions require the estimation of genetic correlations with other economically important traits and the prediction of their selection response. In this study, test-day CH4 emissions were predicted from milk mid-infrared spectra of Holstein cows. Predicted CH4 emissions (PME) and log-transformed CH4 intensity (LMI) computed as the natural logarithm of PME divided by milk yield (MY). Genetic correlations of PME and LMI with traits used currently were approximated from correlations between estimated breeding values of sires. Values were for PME with MY 0.06, fat yield (FY) 0.09, protein yield (PY) 0.13, fertility 0.17; body condition score (BCS) –0.02; udder health (UDH) 0.22; and longevity 0.22. As expected by its definition, values were negative for LMI with production traits (MY –0.61; FY –0.15 and PY –0.40) and positive with fertility (0.36); BCS (0.20); UDH (0.08) and longevity (0.06). The genetic correlations of 33 type traits with PME ranged from –0.12 to 0.25 and for LMI ranged from –0.22 to 0.18. Without selecting PME and LMI (status quo) the relative genetic change through correlated responses of other traits were in PME by 2% and in LMI by –15%, but only due to the correlated response to MY. Results showed for PME that direct selection of this environmental trait would reduce milk carbon foot print but would also affect negatively fertility. Therefore, more profound changes in current indexes will be required than simply adding environmental traits as these traits also affect the expected progress of other traits.

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Genetic analysis of docility score of Australian Angus and Limousin cattle

Animal Production Science ◽

10.1071/an16240 ◽

2018 ◽

Vol 58 (2) ◽

pp. 213 ◽

Cited By ~ 1

Author(s):

S. F. Walkom ◽

M. G. Jeyaruban ◽

B. Tier ◽

D. J. Johnston

Keyword(s):

Adverse Effect ◽

Animal Model ◽

Genetic Analysis ◽

Genetic Parameters ◽

Genetic Correlations ◽

Production Costs ◽

Breeding Value ◽

Maternal Behaviour ◽

Production Traits ◽

Subjective Score

The temperament of cattle is believed to affect the profitability of the herd through impacting production costs, meat quality, reproduction, maternal behaviour and the welfare of the animals and their handlers. As part of the national beef cattle genetic evaluation in Australia by BREEDPLAN, 50 935 Angus and 50 930 Limousin calves were scored by seedstock producers for temperament using docility score. Docility score is a subjective score of the animal’s response to being restrained and isolated within a crush, at weaning, and is scored on a scale from 1 to 5 with 1 representing the quiet and 5 the extremely nervous or anxious calves. Genetic parameters for docility score were estimated using a threshold animal model with four thresholds (five categories) from a Bayesian analysis carried out using Gibbs sampling in THRGIBBS1F90 with post-Gibbs analysis in POSTGIBBSF90. The heritability of docility score on the observed scale was 0.21 and 0.39 in Angus and Limousin, respectively. Since the release of the docility breeding value to the Australian Limousin population there has been a favourable trend within the national herd towards more docile cattle. Weak but favourable genetic correlations between docility score and the production traits indicates that docility score is largely independent of these traits and that selection to improve temperament can occur without having an adverse effect on growth, fat, muscle and reproduction.

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Potential Application of Genomic Technologies in Breeding for Fungal and Oomycete Disease Resistance in Pea

Agronomy ◽

10.3390/agronomy11061260 ◽

2021 ◽

Vol 11 (6) ◽

pp. 1260

Author(s):

Ambuj B. Jha ◽

Krishna K. Gali ◽

Zobayer Alam ◽

V. B. Reddy Lachagari ◽

Thomas D. Warkentin

Keyword(s):

Disease Resistance ◽

Genome Sequence ◽

Potential Application ◽

Ascochyta Blight ◽

Gene Families ◽

Snp Markers ◽

Growth And Yield ◽

Current Status ◽

Genomic Technologies ◽

Sequencing Platforms

Growth and yield of pea crops are severely affected by various fungal diseases, including root rot, Ascochyta blight, powdery mildew, and rust, in different parts of the world. Conventional breeding methods have led to enhancement of host plant resistance against these diseases in adapted cultivars, which is the primary option to minimize the yield losses. To support the breeding programs for marker-assisted selection, several successful attempts have been made to detect the genetic loci associated with disease resistance, based on SSR and SNP markers. In recent years, advances in next-generation sequencing platforms, and resulting improvements in high-throughput and economical genotyping methods, have been used to make rapid progress in identification of these loci. The first reference genome sequence of pea was published in 2019 and provides insights on the distribution and architecture of gene families associated with disease resistance. Furthermore, the genome sequence is a resource for anchoring genetic linkage maps, markers identified in multiple studies, identification of candidate genes, and functional genomics studies. The available pea genomic resources and the potential application of genomic technologies for development of disease-resistant cultivars with improved agronomic profile will be discussed, along with the current status of the arising improved pea germplasm.

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The incorporation of fertility indices in genetic improvement programmes

BSAP Occasional Publication ◽

10.1017/s0263967x00033711 ◽

2001 ◽

Vol 26 (1) ◽

pp. 237-249 ◽

Cited By ~ 28

Author(s):

J.E. Pryce ◽

R.F. Veerkamp

Keyword(s):

Genetic Variance ◽

Selection Index ◽

Genetic Correlations ◽

Live Weight ◽

Parameter Estimates ◽

Phenotypic Variance ◽

Production Traits ◽

Genetic Progress ◽

Detection Rates ◽

Days Open

AbstractIn recent years there has been considerable genetic progress in milk production. Yet, increases in yield have been accompanied by an apparent lengthening of calving intervals, days open, days to first heat and a decline in conception rates, which appears to be both at the genetic and phenotypic level. Fertility has a high relative economic value compared to production traits such as protein, making it attractive to include in a breeding programme. To do this there needs to be genetic variance in fertility. Measures of fertility calculated from service dates have a small genetic compared to phenotypic variance, hence heritability estimates are small, typically less than 5%, although coefficients of genetic variance are comparable to those of production traits. Heritabilities of commencement of luteal activity determined using progesterone profiles are generally higher, and have been reported as being from 0.16 to 0.28, which could be because of a more precise quantification of genetic variance, as management influences such as delaying insemination and heat detection rates are excluded. However, it might not be the use of progesterone profiles alone, as days to first heat observed by farm staff has a heritability of 0.15. The most efficient way to breed for improved fertility is to construct a selection index using the genetic and phenotypic parameter estimates of all traits of interest in addition to their respective economic values. Index traits for fertility could include measures such as calving interval, days open, days to first service, or days to first heat but there may also be alternative measures. Examples include traits related to energy balance, such as live weight and condition score (change), both of which have higher heritabilities than fertility measures and have genetic correlations of sufficient magnitude to make genetic progress by using them feasible. To redress the balance between fertility and production, some countries already publish genetic evaluations of fertility including: Denmark, Finland, France, Germany, Israel, The Netherlands, Norway and Sweden.

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Genetic variation in net feed efficiency in Hereford cattle and its association with other production traits

Proceedings of the British Society of Animal Science ◽

10.1017/s1752756200002027 ◽

1999 ◽

Vol 1999 ◽

pp. 47-47

Author(s):

R.M. Herd ◽

S.C. Bishop

Keyword(s):

Growth Rate ◽

Genetic Variation ◽

Feed Intake ◽

Feed Efficiency ◽

Genetic Correlations ◽

Feed Consumption ◽

Production Traits ◽

Performance Measurements ◽

Hereford Cattle ◽

Rate Selection

Net feed efficiency refers to variation in feed consumption between animals net of requirements for maintenance and production, and may be measured as residual feed intake (RFI). Because RFI is independent of liveweight (LW) and growth rate, selection for improved net feed efficiency is likely to reduce feed intake with little change in growth. The purpose of this study was to establish whether there exists genetic variation in RFI in young British Hereford bulls, and to determine the phenotypic and genetic correlations of RFI with key production traits.The data consisted of performance measurements on 540 bull progeny of 154 British Hereford sires, collected over ten 200-day postweaning performance tests conducted between 1979 and 1988. The traits analysed were food intake (FI), 200 to 400-day daily gain (ADG), 400-day weight (W400), predicted carcass lean content (LEAN), lean growth rate (LGR), food conversion ratio (FI/ADG) and lean FCR (LFCR; FI/(ADG x LEAN), described by Bishop (1992).

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