Strawberry fruit shape: quantification by image analysis and QTL detection by genome-wide association analysis

Nagamatsu, Shiro; Tsubone, Masao; Wada, Takahiro; Oku, Koichiro; Mori, Masayuki; Hirata, Chiharu; Hayashi, Atsushi; Tanabata, Takanari; Isobe, Sachiko; Takata, Kinuko; Shimomura, Katsumi

doi:10.1270/jsbbs.19106

Cited by 18 publications

(11 citation statements)

References 45 publications

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“…GWAS is a powerful tool for the detection of SNP markers linked to different traits in strawberry 9,17,28,30,36,37 . Here, based on a large diversity panel, we detected 71 markers associations to major fruit quality breeding targets.…”

Section: Discussionmentioning

confidence: 99%

Exploration of a European-centered strawberry diversity panel provides markers and candidate genes for the control of fruit quality traits

Prohaska,

Rey-Serra,

Petit

et al. 2024

Preprint

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Fruit quality traits are major breeding targets in cultivated strawberry (Fragaria x ananassa). Taking into account the requirements of both growers and consumers when selecting high quality cultivars is a real challenge. Here, we used an original diversity panel enriched with unique European accessions and the 50K FanaSNP array to highlight the evolution of strawberry diversity over the past 160 years, investigate the molecular basis of 12 major fruit quality traits by GWAS, and provide genetic markers for breeding. Results show that considerable improvements of key breeding targets including fruit weight, firmness, composition and appearance occurred simultaneously in European and American populations. Despite the high genetic diversity of our panel, we observed a drop in nucleotide diversity in certain chromosome regions, revealing the impact of selection. GWAS identified 71 associations with 11 quality traits and, while validating known associations (firmness, sugar), highlighted the predominance of new QTL, demonstrating the value of using untapped genetic resources. Three of the six selective sweeps detected are related to glossiness or skin resistance, two little-studied traits important for fruit attractiveness and, potentially, postharvest shelf-life. Moreover, major QTL for firmness, glossiness, skin resistance and susceptibility to bruising are found within a low diversity region of chromosome 3D. Stringent search for candidate genes underlying QTL uncovered strong candidates for fruit color, firmness, sugar and acid composition, glossiness and skin resistance. Overall, our study provides a potential avenue for extending shelf-life without compromising flavor and color as well as the genetic markers needed to achieve this goal.

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Section: Discussionmentioning

confidence: 99%

Exploration of a European-centered strawberry diversity panel provides markers and candidate genes for the control of fruit quality traits

Prohaska,

Rey-Serra,

Petit

et al. 2024

Preprint

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show abstract

“…Although visual evaluation is a widely used nondestructive method for grading and sorting in horticultural crops, utilization of high-throughput phenotyping platforms is essential to obtain robust, faster, and objective results [ 14 ]. Nowadays, quantitative measurement of these traits (color, size, shape, and surface texture) using image analysis is increasingly used in different horticultural crops [ 13 , 84 , 85 , 86 , 87 ].…”

Section: Applications Of Image-based High-throughput Phenotyping In H...mentioning

confidence: 99%

“…RGB and HSI are able to separate within the noir and non-noir groups and enable the identification of minor QTLs controlling grape berry color, which were not identified previously using qualitative evaluation [ 89 ]. Quantitative measurement of strawberry fruit shape based on elliptic Fourier descriptors (EFDs) [ 90 ] and image analysis allowed the identification of two QTLs for shape via a genome-wide association study [ 84 ]. The fruit shape was highly correlated with the fruit length-to-width ratio.…”

Section: Applications Of Image-based High-throughput Phenotyping In H...mentioning

confidence: 99%

Image-Based High-Throughput Phenotyping in Horticultural Crops

Abebe

Kim

et al. 2023

Plants

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Plant phenotyping is the primary task of any plant breeding program, and accurate measurement of plant traits is essential to select genotypes with better quality, high yield, and climate resilience. The majority of currently used phenotyping techniques are destructive and time-consuming. Recently, the development of various sensors and imaging platforms for rapid and efficient quantitative measurement of plant traits has become the mainstream approach in plant phenotyping studies. Here, we reviewed the trends of image-based high-throughput phenotyping methods applied to horticultural crops. High-throughput phenotyping is carried out using various types of imaging platforms developed for indoor or field conditions. We highlighted the applications of different imaging platforms in the horticulture sector with their advantages and limitations. Furthermore, the principles and applications of commonly used imaging techniques, visible light (RGB) imaging, thermal imaging, chlorophyll fluorescence, hyperspectral imaging, and tomographic imaging for high-throughput plant phenotyping, are discussed. High-throughput phenotyping has been widely used for phenotyping various horticultural traits, which can be morphological, physiological, biochemical, yield, biotic, and abiotic stress responses. Moreover, the ability of high-throughput phenotyping with the help of various optical sensors will lead to the discovery of new phenotypic traits which need to be explored in the future. We summarized the applications of image analysis for the quantitative evaluation of various traits with several examples of horticultural crops in the literature. Finally, we summarized the current trend of high-throughput phenotyping in horticultural crops and highlighted future perspectives.

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“…However, the researchers reported that two QTLs were mapped in LGIII and LGIV for the neck without achenes regions. On the other hand, Nagamatsu et al [56] conducted a study in order to identify QTLs associated with fruit shape using a MAGIC population derived from full-sib families. In genome-wide association analysis, QTL regions were detected within chromosomes 6 and 7 in genome-wide association analysis.…”

Section: Qtls Related To the Morphological And Biochemical Traits In ...mentioning

confidence: 99%

Quantitative Trait Loci Associated with Agronomical Traits in Strawberry

Karcı¹,

Tevfik²,

Kafkas³

et al. 2023

Recent Studies on Strawberries

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The cultivated strawberry (Fragaria x ananassa) is derived from Fragaria chiloensis and Fragaria virginiana species a few centuries ago, and it is one of the most preferred and consumed berries all over the world because of its a good source in terms of many nutritional elements. Strawberry has high genetic variability and adaptation to different environmental conditions due to its highly heterozygous nature. In the last decades, many farmers, breeders, researchers even consumers have started to focus on berry quality traits such as large fruit, uniform shape, high fruit firmness, high fruit sensorial quality (aroma contents), color, gloss, and resistance to pathogens. Thus, the development of novel strawberry cultivars or genotypes with high nutritionally quality traits has become one of the main aims in strawberry breeding programs. Biotechnological tools such as the identification of quantitative trait loci (QTL) and marker-assisted selection (MAS) are the most widely used technologies in fruit breeding programs for shortening the breeding period. Identification of QTLs in agnomical important traits are very valuable tools for early selection in strawberry breeding programs. This chapter is focused on QTL and marker assisted breeding studies in strawberry to date and provides new perspectives on molecular breeding in strawberry breeding.

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Strawberry fruit shape: quantification by image analysis and QTL detection by genome-wide association analysis

Cited by 18 publications

References 45 publications

Exploration of a European-centered strawberry diversity panel provides markers and candidate genes for the control of fruit quality traits

Exploration of a European-centered strawberry diversity panel provides markers and candidate genes for the control of fruit quality traits

Image-Based High-Throughput Phenotyping in Horticultural Crops

Quantitative Trait Loci Associated with Agronomical Traits in Strawberry

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