Automatic estimation of wheat grain morphometry from computed tomography data
Harry Strange A D , Reyer Zwiggelaar A , Craig Sturrock B , Sacha J. Mooney B and John H. Doonan CA Department of Computer Science, Aberystwyth University, Aberystwyth, SY23 3DB, UK.
B School of Biosciences, University of Nottingham, Sutton Bonnington, LE12 5RD, UK.
C National Plant Phenomics Center, Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, SY23 3EB, UK.
D Corresponding author. Email: hgs08@aber.ac.uk
Functional Plant Biology 42(5) 452-459 https://doi.org/10.1071/FP14068
Submitted: 28 February 2014 Accepted: 12 August 2014 Published: 5 November 2014
Abstract
Wheat (Triticum aestivum L.) grain size and morphology are playing an increasingly important role as agronomic traits. Whole spikes from two disparate strains, the commercial type Capelle and the landrace Indian Shot Wheat, were imaged using a commercial computed tomography system. Volumetric information was obtained using a standard back-propagation approach. To extract individual grains within the spikes, we used an image processing pipeline that included adaptive thresholding, morphological filtering, persistence aspects and volumetric reconstruction. This is a fully automated, data-driven pipeline. Subsequently, we extracted several morphometric measures from the individual grains. Taking the location and morphology of the grains into account, we show distinct differences between the commercial and landrace types. For example, average volume is significantly greater for the commercial type (P = 0.0024), as is the crease depth (P = 1.61 × 10−5). This pilot study shows that the fully automated approach described can retain developmental information and reveal new morphology information at an individual grain level.
Additional keywords: grain analysis morphometric measurements, segmentation.
References
Brown TA, Jones MK, Powell W, Allaby RG (2009) The complex origins of domesticated crops in the Fertile Crescent. Trends in Ecology & Evolution 24, 103–109.| The complex origins of domesticated crops in the Fertile Crescent.Crossref | GoogleScholarGoogle Scholar |
Dice LR (1945) Measures of the amount of ecologic association between species. Ecology 26, 297–302.
| Measures of the amount of ecologic association between species.Crossref | GoogleScholarGoogle Scholar |
Doehlert DC, McMullen MS, Jannink J-L (2006) Oat grain/groat size: a physical basis for test weight. Cereal Chemistry 83, 114–118.
| Oat grain/groat size: a physical basis for test weight.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD28Xms1ClsQ%3D%3D&md5=679487e61fefce9bca79b14d0861a3bbCAS |
Dubcovsky J, Dvorak J (2007) Genome plasticity a key factor in the success of polyploid wheat under domestication. Science 316, 1862–1866.
| Genome plasticity a key factor in the success of polyploid wheat under domestication.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD2sXmvV2mu7k%3D&md5=9164b35967e50829fe22cb4b35b58276CAS | 17600208PubMed |
Evers AD, Cox RI, Shaheedullah MZ, Withey RP (1990) Predicting milling extraction rate by image analysis of wheat grains. Aspects of Applied Biology 25, 417–426.
Fuller DQ (2007) Contrasting patterns in crop domestication and domestication rates: recent archaeobotanical insights from the Old World. Annals of Botany 100, 903–924.
| Contrasting patterns in crop domestication and domestication rates: recent archaeobotanical insights from the Old World.Crossref | GoogleScholarGoogle Scholar | 17495986PubMed |
Gegas VC, Nazari A, Griffiths S, Simmonds J, Fish L, Orford S, Sayers L, Doonan JH, Snape JW (2010) A genetic framework for grain size and shape variation in wheat. The Plant Cell 22, 1046–1056.
| A genetic framework for grain size and shape variation in wheat.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC3cXnsV2isr4%3D&md5=c094af84a6ccad38b2105625dc55eab8CAS | 20363770PubMed |
Groos C, Robert N, Bervas E, Charmet G (2003) Genetic analysis of grain protein-content, grain yield and thousand-kernel weight in bread wheat. Theoretical and Applied Genetics 106, 1032–1040.
Kirby EJM, Appleyard M (1987). ‘Cereal development guide.’ (NAC Cereal Unit: Stoneleigh, Kenilworth)
Kovach MJ, Sweeney MT, McCouch SR (2007) New insights into the history of rice domestication. Trends in Genetics 23, 578–587.
| New insights into the history of rice domestication.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD2sXht12gurrK&md5=4a102aa4c422848d2e0e11485fef6afeCAS | 17963977PubMed |
Langer RHM, Hanif M (1973) Study of floret development in wheat (Triticum aestivum L.). Annals of Botany 37, 743–751.
Ma Z, Zhao D, Zhang C, Zhang Z, Xue S, Lin F, Kong Z, Tian D, Luo Q (2007) Molecular genetic analysis of five spike-related traits in wheat using RIL and immortalized F2 populations. Molecular Genetics and Genomics 277, 31–42.
| Molecular genetic analysis of five spike-related traits in wheat using RIL and immortalized F2 populations.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD28XhtlWntbzP&md5=eedd31f36aaf9cef7a10959249a74296CAS | 17033810PubMed |
McMaster GS (1997) Phenology, development, and growth of the wheat (Triticum aestivum L.) shoot apex: a review. Advances in Agronomy 59, 63–118.
| Phenology, development, and growth of the wheat (Triticum aestivum L.) shoot apex: a review.Crossref | GoogleScholarGoogle Scholar |
Otsu N (1979) A threshold selection method from gray-level histograms. IEEE Transactions on Systems, Man, and Cybernetics 9, 62–66.
| A threshold selection method from gray-level histograms.Crossref | GoogleScholarGoogle Scholar |
Russell BC, Torralba A, Murphy KP, Freeman WT (2008) LabelMe: a database and web-based tool for image annotation. International Journal of Computer Vision 77, 157–173.
| LabelMe: a database and web-based tool for image annotation.Crossref | GoogleScholarGoogle Scholar |
Soille P (2004) ‘Morphological image analysis.’ 2nd edn. (Springer-Verlag: Berlin)
Sun J, Huang K, Li W, Wang L, Wang A, Huo J, Chen J, Chen C (2007) Effects of wheat flour fortified with different iron fortificants on iron status and anemia prevalence in iron deficient anemic students in Northern China. Asia Pacific Journal of Clinical Nutrition 16, 116–121.
Wychowaniec J, Griffiths I, Mughal A, Gay A (2013) Compaction of cereal grain. Philosophical Magazine 93, 4151–4158.
| Compaction of cereal grain.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC3sXpslGhsr8%3D&md5=ac0e93792e8d9c501effb33439e9ab1bCAS |
