Selecting for multiple traits in complex production systems: A case study of sugarcane in China

Yang, Kun; Jackson, P.; Wei, Xianming; Chen, Xuekuan; Liu, Jiayong; Zhao, Jietang; CaiWen, Wu; YuanHong, Fan

doi:10.1016/j.agsy.2016.12.010

Cited by 4 publications

(13 citation statements)

References 6 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Briefly, every year, crosses between accessions generate hundreds of thousands of F1 progenies, and the individuals reaching the final stages of selection are commonly evaluated over several harvests in multienvironment trials (METs) to identify those with the potential to become new cultivars [10–13]. Even with the adoption of better agricultural practices and selection strategies in the early stages of breeding programs, which attempt to measure and isolate the environmental effects of genetic factors [13–16], the genetic gains to quantitative traits have declined in recent years for sugarcane and other crops [17–19].…”

Section: Introductionmentioning

confidence: 99%

A genome-wide association study identified loci for yield component traits in sugarcane (Saccharum spp.)

et al. 2019

View full text Add to dashboard Cite

Sugarcane ( Saccharum spp.) has a complex genome with variable ploidy and frequent aneuploidy, which hampers the understanding of phenotype and genotype relations. Despite this complexity, genome-wide association studies (GWAS) may be used to identify favorable alleles for target traits in core collections and then assist breeders in better managing crosses and selecting superior genotypes in breeding populations. Therefore, in the present study, we used a diversity panel of sugarcane, called the Brazilian Panel of Sugarcane Genotypes (BPSG), with the following objectives: (i) estimate, through a mixed model, the adjusted means and genetic parameters of the five yield traits evaluated over two harvest years; (ii) detect population structure, linkage disequilibrium (LD) and genetic diversity using simple sequence repeat (SSR) markers; (iii) perform GWAS analysis to identify marker-trait associations (MTAs); and iv) annotate the sequences giving rise to SSR markers that had fragments associated with target traits to search for putative candidate genes. The phenotypic data analysis showed that the broad-sense heritability values were above 0.48 and 0.49 for the first and second harvests, respectively. The set of 100 SSR markers produced 1,483 fragments, of which 99.5% were polymorphic. These SSR fragments were useful to estimate the most likely number of subpopulations, found to be four, and the LD in BPSG, which was stronger in the first 15 cM and present to a large extension (65 cM). Genetic diversity analysis showed that, in general, the clustering of accessions within the subpopulations was in accordance with the pedigree information. GWAS performed through a multilocus mixed model revealed 23 MTAs, six, three, seven, four and three for soluble solid content, stalk height, stalk number, stalk weight and cane yield traits, respectively. These MTAs may be validated in other populations to support sugarcane breeding programs with introgression of favorable alleles and marker-assisted selection.

show abstract

Section: Introductionmentioning

confidence: 99%

A genome-wide association study identified loci for yield component traits in sugarcane (Saccharum spp.)

et al. 2019

View full text Add to dashboard Cite

show abstract

“…Implications of applying a multi-traits indirect selection index have been studied and reviewed extensively in cereals [24]. In sugarcane, Yang et al [25] provided a theoretical assessment of applying a multi-trait selection system in conventional breeding in China and predicted their value across the production chain. However, optimal selection indices based on indirect traits are not widely applied in breeding programs, partly due to the practical difficulties in measuring multiple traits from a large number of clones in large-scale breeding programs.…”

Section: Introductionmentioning

confidence: 99%

High-Throughput Phenotyping of Indirect Traits for Early-Stage Selection in Sugarcane Breeding

et al. 2019

Self Cite

View full text Add to dashboard Cite

One of the major limitations for sugarcane genetic improvement is the low heritability of yield in the early stages of breeding, mainly due to confounding inter-plot competition effects. In this study, we investigate an indirect selection index (Si), developed based on traits correlated to yield (indirect traits) that were measured using an unmanned aerial vehicle (UAV), to improve clonal assessment in early stages of sugarcane breeding. A single-row early-stage clonal assessment trial, involving 2134 progenies derived from 245 crosses, and a multi-row experiment representative of pure-stand conditions, with an unrelated population of 40 genotypes, were used in this study. Both experiments were screened at several stages using visual, multispectral, and thermal sensors mounted on a UAV for indirect traits, including canopy cover, canopy height, canopy temperature, and normalised difference vegetation index (NDVI). To construct the indirect selection index, phenotypic and genotypic variance-covariances were estimated in the single-row and multi-row experiment, respectively. Clonal selection from the indirect selection index was compared to single-row yield-based selection. Ground observations of stalk number and plant height at six months after planting made from a subset of 75 clones within the single-row experiment were highly correlated to canopy cover (rg = 0.72) and canopy height (rg = 0.69), respectively. The indirect traits had high heritability and strong genetic correlation with cane yield in both the single-row and multi-row experiments. Only 45% of the clones were common between the indirect selection index and single-row yield based selection, and the expected efficiency of correlated response to selection for pure-stand yield based on indirect traits (44%–73%) was higher than that based on single-row yield (45%). These results highlight the potential of high-throughput phenotyping of indirect traits combined in an indirect selection index for improving early-stage clonal selections in sugarcane breeding.

show abstract

“…Details of traits determined by measurement or observation during the experiments, together with the units for each trait, were described by Yang et al. (2017) with brief details given in Table 1.…”

Section: Methodsmentioning

confidence: 99%

“…The economic weightings applied to each trait (Table 2) were based on results presented by Yang et al. (2017), with one exception as follows.…”

Section: Methodsmentioning

confidence: 99%

See 1 more Smart Citation

Optimizing selection indices in sugarcane seedlings

et al. 2021

Self Cite

View full text Add to dashboard Cite

Selection of superior clones in sugarcane (Saccharum spp.) breeding programs follows a multistage process, starting in the first stage with selection of seedlings grown from seeds obtained from crosses. Effective selection of seedlings is important but notoriously difficult. Selection validity is affected by experimental error variation and interplant competition effects and is also complicated by the need to consider many different traits that affect economic value of cultivars (e.g., cane yield, sugar content, fiber content, disease resistance, etc.). In this study, we developed an optimized protocol for selection of sugarcane seedlings that balances the desire to maximize genetic gains but also be cost and labor efficient. A population of seedlings in commercial sugarcane breeding programs was first evaluated in a field trial (Stage 1). A subset of the population was then taken at random and grown in a subsequent trial (Stage 2) for evaluation in small plots. Minor modifications to application of the complete selection index that would greatly reduce labor requirements but have only a small impact on reducing genetic gains were then explored, to identify optimal selection protocols for routine application in commercial breeding programs. A procedure is recommended for routine selection of seedlings that involves (a) selection of families based on an index of four traits (stalk diameter, stalk height, trashiness, and pith rating, all derived from measurements of a small sample of seedlings in each family), followed by (b) sequential measurement and culling of individual seedlings in each selected family based on (in order) trashiness, stalk diameter, and pith rating.

show abstract

Selecting for multiple traits in complex production systems: A case study of sugarcane in China

Cited by 4 publications

References 6 publications

A genome-wide association study identified loci for yield component traits in sugarcane (Saccharum spp.)

A genome-wide association study identified loci for yield component traits in sugarcane (Saccharum spp.)

High-Throughput Phenotyping of Indirect Traits for Early-Stage Selection in Sugarcane Breeding

Optimizing selection indices in sugarcane seedlings

Contact Info

Product

Resources

About