Sugarcane Breeding in Australia

Wei, Xianming; Eglinton, J.; Piperidis, George; Atkin, Felicity; Morgan, T.; Parfitt, Roy; Hu, Fengduo

doi:10.1007/s12355-021-00969-5

Cited by 12 publications

(17 citation statements)

References 9 publications

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“…However, most clonally propagated crops are polyploid and highly heterozygous, particularly sugarcane. As a result, effectively all gametes produced by any parental genotype are distinct, and all F 1 descendants are unique (Wei et al 2021). The overall genetic (additive/non-additive) effects could be used to develop new varieties.…”

Section: Discussionmentioning

confidence: 99%

“…Sugarcane breeding programs were initiated from crosses between sugar-rich cultivated species, primarily Saccharum Officinarum L ., and a wild relative, Saccharum Spontaneum L ., which provided disease/pest resistance and abiotic tolerance in a range of varieties (Wei and Jackson 2016; Yadav et al 2020). In modern commercial programs, the emphasis on sugarcane breeding has shifted to crossing highly heterozygous inter-specific hybrids (Wei et al 2021). The primary objective of this shift is to create genetic variation that can be exploited via selection in the subsequent cycles before reverting to clonal selection.…”

Section: Introductionmentioning

confidence: 99%

“…Genomic selection (GS) can reduce the breeding cycle by allowing the quick selection of superior genotypes at any stage of the sugarcane breeding program (Voss-Fels et al 2021). Typically, truncation selection is the first step in GS-assisted breeding programs where high-performing parental clones are selected based on the GEBVs, which are crossed at random to produce the next generation, ensuring that the progenies have a high mean performance (Wei et al 2021). However, in the presence of non-additive effects, the mean performance of progeny in a clonal breeding program can deviate from the mean breeding value of the parents.…”

Section: Introductionmentioning

confidence: 99%

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Genomic mate-allocation strategies exploiting additive and non-additive genetic effects to maximise total clonal performance in sugarcane

Yadav¹,

Ross

Wei

et al. 2022

Preprint

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Mate-allocation in breeding programs can improve progeny performance by exploiting non-additive effects. Breeding decisions in the mate-allocation approach are based on predicted progeny merit rather than parental breeding value. This is particularly attractive when non-additive effects are significant, and the best-predicted progeny can be clonally propagated, for example sugarcane. We compared mate-allocation strategies that leverage non-additive and heterozygosity effects to maximise sugarcane clonal performance to schemes that use only additive effects to maximise breeding value. We used phenotypes and genotypes from a population of 2,909 clones phenotyped in Australian sugarcane breeding final assessment trials for three traits: tonnes of cane per hectare (TCH), commercial cane sugar (CCS), and fibre. The clones from the last generation of this data set were used as parents to simulate families from all possible crosses (1,225), each with 50 progenies. The breeding and clonal values of progeny were predicted using GBLUP (considering only additive effects) and the e-GBLUP model (incorporating additive, non-additive and heterozygosity effects). Integer linear programming was used to identify the optimal mate-allocation among the selected parents. Compared to the breeding value, the predicted progeny value of allocated crossing pairs based on clonal performance (e-GBLUP) increased by 57%, 12%, and 16% for TCH, CCS, and fibre, respectively. In our study, the mate-allocation strategy exploiting non-additive and heterozygosity effects resulted in better clonal performance. However, there was a noticeable decline in additive gain, particularly for TCH, which might have been caused by the presence of large epistatic effects. When crosses were chosen based on clonal performance for TCH, the inbreeding coefficient of progeny was significantly lower than for random mating, indicating that utilising non-additive and heterozygosity effects has advantages for controlling inbreeding depression. Therefore, mate-allocation is recommended in clonal crops to improve clonal performance and reduce inbreeding.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Genomic mate-allocation strategies exploiting additive and non-additive genetic effects to maximise total clonal performance in sugarcane

Yadav¹,

Ross

Wei

et al. 2022

Preprint

Self Cite

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“…Although the whole-genome sequence of S. spontaneum (Zhang et al, 2018) and a monoploid sequence of a commercial cultivar, R570 (Olivier et al, 2018), have been released, the large and complex genome structure of modern sugarcane hybrids makes genetic and genomic studies, including breeding of sugarcane very challenging. This is reflected in the long history of molecular marker research, yet development of large-scale practically useful 1 http://sugarcane.org/sugarcaneproducts/ethanol molecular markers for commercial breeding is only now becoming a significant research area, and that too restricted to a very few major sugarcane breeding programs worldwide (Aitken, 2021;Cursi et al, 2021;Ram et al, 2021;Wei et al, 2021).…”

Section: Introductionmentioning

confidence: 99%

“…This is reflected in the long history of molecular marker research, yet development of large-scale practically useful molecular markers for commercial breeding is only now becoming a significant research area, and that too restricted to a very few major sugarcane breeding programs worldwide ( Aitken, 2021 ; Cursi et al, 2021 ; Ram et al, 2021 ; Wei et al, 2021 ).…”

Section: Introductionmentioning

confidence: 99%

Quantitative Trait Loci Mapping and Development of KASP Marker Smut Screening Assay Using High-Density Genetic Map and Bulked Segregant RNA Sequencing in Sugarcane (Saccharum spp.)

et al. 2022

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Sugarcane is one of the most important industrial crops globally. It is the second largest source of bioethanol, and a major crop for biomass-derived electricity and sugar worldwide. Smut, caused by Sporisorium scitamineum, is a major sugarcane disease in many countries, and is managed by smut-resistant varieties. In China, smut remains the single largest constraint for sugarcane production, and consequently it impacts the value of sugarcane as an energy feedstock. Quantitative trait loci (QTLs) associated with smut resistance and linked diagnostic markers are valuable tools for smut resistance breeding. Here, we developed an F1 population (192 progeny) by crossing two sugarcane varieties with contrasting smut resistance and used for genome-wide single nucleotide polymorphism (SNP) discovery and mapping, using a high-throughput genotyping method called “specific locus amplified fragment sequencing (SLAF-seq) and bulked-segregant RNA sequencing (BSR-seq). SLAF-seq generated 148,500 polymorphic SNP markers. Using SNP and previously identified SSR markers, an integrated genetic map with an average 1.96 cM marker interval was produced. With this genetic map and smut resistance scores of the F1 individuals from four crop years, 21 major QTLs were mapped, with a phenotypic variance explanation (PVE) > 8.0%. Among them, 10 QTLs were stable (repeatable) with PVEs ranging from 8.0 to 81.7%. Further, four QTLs were detected based on BSR-seq analysis. aligning major QTLs with the genome of a sugarcane progenitor Saccharum spontaneum, six markers were found co-localized. Markers located in QTLs and functional annotation of BSR-seq-derived unigenes helped identify four disease resistance candidate genes located in major QTLs. 77 SNPs from major QTLs were then converted to Kompetitive Allele-Specific PCR (KASP) markers, of which five were highly significantly linked to smut resistance. The co-localized QTLs, candidate resistance genes, and KASP markers identified in this study provide practically useful tools for marker-assisted sugarcane smut resistance breeding.

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Five decades of productivity gains in the Louisiana sugar industry

Blanchard,

Taylor,

Pontif

et al. 2023

Crop Science

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This study analyzed trends across five decades of productivity data from the Louisiana Sugar Industry, from 1969 to 2021, for sucrose content, cane yield, and sugar yield. Trends over the five decades were revealed using robust regression models, and the least square means allowed for decade‐wise comparisons of trends. Sucrose content increased 45%, from 80.9 ± 6.4 g kg−1 in the first (1969‐1979) to 116.7 ± 4.8 g kg−1 in the fifth (2010‐2021) decade, at 0.85 ± 0.06 g kg−1 per year. Cane yield increased slower (32.2%), from 57.7 ± 5.9 Mg ha −1 in the first to 76.3 ± 6.3 Mg ha−1 in the fifth decade, at 0.45 ± 0.07 Mg ha−1 per year. Sugar yield increased 93% from the first (4.6 ± Mg ha−1) to the fifth (8.9 ± 0.76 Mg ha−1) decade at 0.1 ± 0.01 Mg ha−1 per year. The gains were neither significant nor consistent when comparing successive decades, incremental rather than rapid, and maintained once achieved. Significant (p < 0.05) gains in all traits occurred only in the third decade (1990‐1999) with yearly increases of 1.15 ± 0.30 g kg−1 for sucrose content, 3.00 ± 0.27 Mg ha −1 for cane yield, and 0.35 ± 0.05 Mg ha−1 for sugar yield. Comparisons of trait means between successive decades found both significant (p < 0.05) and non‐significant (p > 0.05) differences, however, comparisons between non‐contiguous decades were all significant (p < 0.05). Variety development accounted for 60% of the progress with sucrose content contributing more (10% more) compared with cane yield. The Louisiana sugar industry has experienced substantial productivity gains in the last five decades thanks to a combination of factors with variety development being the most impactful.This article is protected by copyright. All rights reserved

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Sugarcane Breeding in Australia

Cited by 12 publications

References 9 publications

Genomic mate-allocation strategies exploiting additive and non-additive genetic effects to maximise total clonal performance in sugarcane

Genomic mate-allocation strategies exploiting additive and non-additive genetic effects to maximise total clonal performance in sugarcane

Quantitative Trait Loci Mapping and Development of KASP Marker Smut Screening Assay Using High-Density Genetic Map and Bulked Segregant RNA Sequencing in Sugarcane (Saccharum spp.)

Five decades of productivity gains in the Louisiana sugar industry

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