Genome-wide association study of drought tolerance in cassava

Silva, Priscila Patrícia dos Santos; Sousa, Massáine Bandeira e; Oliveira, Eder Jorge de; Morgante, Carolina Vianna; Oliveira, Carlos Roberto Silva de; Vieira, Simone Leal; Borel, Jerônimo Constantino

doi:10.1007/s10681-021-02800-4

Cited by 14 publications

(9 citation statements)

References 73 publications

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“…Only root angle and crown diameter parameters, which could be retrieved from 2D photos, have been used to represent CRC data 12 . Furthermore, genome-wide association studies of cassava root traits reported to date only relied on individual root data and none of the whole crown parameters 9 , 10 , 41 , 42 . It is apparent that cassava phenotyping is limited to direct measurements and 2D data, and the whole crowns have never been studied due to limited tools.…”

Section: Discussionmentioning

confidence: 99%

Cassava root crown phenotyping using three-dimension (3D) multi-view stereo reconstruction

Sunvittayakul

Kittipadakul

Wonnapinij

et al. 2022

Sci Rep

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Phenotypic analysis of cassava root crowns (CRCs) so far has been limited to visual inspection and very few measurements due to its laborious process in the field. Here, we developed a platform for acquiring 3D CRC models using close-range photogrammetry for phenotypic analysis. The state of the art is a low cost and easy to set up 3D acquisition requiring only a background sheet, a reference object and a camera, compatible with field experiments in remote areas. We tested different software with CRC samples, and Agisoft and Blender were the most suitable software for generating high-quality 3D models and data analysis, respectively. We optimized the workflow by testing different numbers of images for 3D reconstruction and found that a minimum of 25 images per CRC can provide high quality 3D models. Up to ten traits, including 3D crown volumes, 3D crown surface, root density, surface-to-volume ratio, root numbers, root angle, crown diameter, cylinder soil volume, CRC compactness and root length can be extracted providing novel parameters for studying cassava storage roots. We applied this platform to partial-inbred cassava populations and demonstrated that our platform provides reliable 3D CRC modelling for phenotypic analysis, analysis of genetic variances and supporting breeding selection.

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Section: Discussionmentioning

confidence: 99%

Cassava root crown phenotyping using three-dimension (3D) multi-view stereo reconstruction

Sunvittayakul

Kittipadakul

Wonnapinij

et al. 2022

Sci Rep

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“…Genome-wide association study (GWAS) has been an effective approach to dissect the genetic architecture of complex traits, such as water deficit tolerance [27]. Several GWAS in soybean, barley, cassava and wheat have been carried out to study the genetic factors underlying water deficit tolerance employing drought tolerance index (DTI) parameter to identify genomic regions that control this complex trait [28][29][30][31]. The DTI is a robust indicator of both genotypic superiority and stability across moisture regimes, and the loci associated with this parameter confer both high yield potential and water deficit tolerance [31,32].…”

Section: Introductionmentioning

confidence: 99%

Genomic regions associated with physiological, biochemical and yield-related responses under water deficit in diploid potato at the tuber initiation stage revealed by GWAS

et al. 2021

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Water deficit, which is increasing with climate change, is a serious threat to agricultural sustainability worldwide. Dissection of the genetic architecture of water deficit responses is highly desirable for developing water-deficit tolerant potato cultivars and enhancing the resilience of existing cultivars. This study examined genetic variation in response to water deficit in a panel of diploid potato and identified the QTL governing this trait via a genome-wide association study (GWAS). A panel of 104 diploid potato accessions were evaluated under both well-watered and water deficit treatments at tuber initiation stage. Drought stress index (DTI) was calculated to assess tolerance of the diploid potato genotypes to water deficit. The GWAS was conducted using a matrix of 47K single nucleotide polymorphisms (SNP), recently available for this population. We are reporting 38 QTL, seven for well-watered conditions, twenty-two for water deficit conditions and nine for DTI which explain between 12.6% and 44.1% of the phenotypic variance. A set of 6 QTL were found to be associated with more than one variable. Marker WDP-9.21 was found associated with tuber fresh weigh under WD and gene annotation analysis revealed co-localization with the Glucan/water dikinase (GWD) gene. Of the nine QTL detected from DTI on chromosomes 2,3,5,8,10 and 12, three candidate genes with a feasible role in water deficit response were identified. The findings of this study can be used in marker-assisted selection (MAS) for water- deficit tolerance breeding in potato.

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“…Advanced testing is usually done in multienvironment trials, including low rainfall, heat-stressed environments ( Hershey, 1984 ). Although genetic control of drought tolerance in cassava, as measured by yield under drought, is complex with strong genotype-by-environment interaction ( de Oliveira et al, 2015 ), a recent GWAS identified candidate genes with known association to drought tolerance and markers useful for breeding ( dos Santos Silva et al, 2021 ).…”

Section: Can We Develop Climate-resilient Crops?mentioning

confidence: 99%

Climate change challenges, plant science solutions

et al. 2022

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Climate change is a defining challenge of the 21st century, and this decade is a critical time for action to mitigate the worst effects on human populations and ecosystems. Plant science can play an important role in developing crops with enhanced resilience to harsh conditions (e.g., heat, drought, salt stress, flooding, disease outbreaks) and engineering efficient carbon-capturing and carbon-sequestering plants. Here, we present examples of research being conducted in these areas and discuss challenges and open questions as a call to action for the plant science community.

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Genome-wide association study of drought tolerance in cassava

Cited by 14 publications

References 73 publications

Cassava root crown phenotyping using three-dimension (3D) multi-view stereo reconstruction

Cassava root crown phenotyping using three-dimension (3D) multi-view stereo reconstruction

Genomic regions associated with physiological, biochemical and yield-related responses under water deficit in diploid potato at the tuber initiation stage revealed by GWAS

Climate change challenges, plant science solutions

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