Crop Seed Phenomics: Focus on Non-Destructive Functional Trait Phenotyping Methods and Applications

Seeds play a critical role in ensuring food security for the earth's 8 billion people. There is great biodiversity in plant seed content traits worldwide. Consequently, the development of robust, rapid, and high-throughput methods is required for seed quality evaluation and acceleration of crop improvement. There has been considerable progress in the past 20 years in various non-destructive methods to uncover and understand plant seed phenomics. This review highlights recent advances in non-destructive seed phenomics techniques, including Fourier Transform near infrared (FT-NIR), Dispersive-Diode Array (DA-NIR), Single-Kernel (SKNIR), Micro-Electromechanical Systems (MEMS-NIR) spectroscopy, Hyperspectral Imaging (HSI), and Micro-Computed Tomography Imaging (micro-CT). The potential applications of NIR spectroscopy are expected to continue to rise as more seed researchers, breeders, and growers successfully adopt it as a powerful non-destructive method for seed quality phenomics. It will also discuss the advantages and limitations that need to be solved for each technique and how each method could help breeders and industry with trait identification, measurement, classification, and screening or sorting of seed nutritive traits. Finally, this review will focus on the future outlook for promoting and accelerating crop improvement and sustainability.

Effects of protein digestion on in vitro digestibility of starch in sorghum differing in endosperm hardness and flour particle size

In vitro digestibility of starch in sorghum grains differing in endosperm hardness and flour particle size was investigated. The starch digestibility increased as the particle size of flour decreased, but no clear trend was observed in digestibility of starch in sorghum flours milled from grains with different hardness. The protein matrix affected the digestion of starch. The pH value (2.0 vs. 1.3) was a critical factor affecting protein digestion. Optimum pH (pH 2.0 for pepsin) digested more protein, resulting in a greater digestion of starch. Resistant starch (RS) content was 8.5-26.3% in isolated sorghum starch but higher (10.6-29.5%) in sorghum flours. Protein digestibility decreased after cooking while starch digestibility increased compared to native sorghum flours; disulfide bonds formed between protein molecules. RS content of cooked sorghum flour was much higher without pepsin treatment (16.93-23.99%) than that of cooked sorghum flour with pepsin treatment (4.86-12.53%).

Divergence in Single Kernel Characteristics and Grain Nutritional Profiles of Wheat Genetic Resource and Association Among Traits

Triticum aestivum is among the few species of crops which has been widely grown as a source of food. For seed quality trait analysis, wheat germplasm (77 genotypes) was collected from Pakistan's diverse agro-climatic regions. Significant variation (p < 0.05) was observed for tested parameters among tested genotypes. Genotypes with maximum protein content, i.e., GA2002 (16.5%) and Marvi (16.5%), moisture content, i.e., advance line 9,244 (11%), starch content, i.e., AARI 2011 (54.1%), zeleny sedimentation rate, i.e., advance line 2006 (44ml), wet gluten content, i.e., advance line 2006 (44%), kernel weight, i.e., advance line TC-4928 (41.6 ± 9.5 mg), kernel diameter, i.e., sassui (2.91 ± 0.32 mm), kernel moisture, i.e., AUQAB 2000 (11.7 ± 0.4%), Mairaj 2000 (11.7 ± 0.4%), and Barani-83 (11.7 ± 0.3%), and hardness index, i.e., Punjab 2011 (91 ± 39) are concluded as potential candidates to be explored for bakery products and the breeding program to improve quality attributes of wheat. Data were also analyzed for correlation, agglomerative hierarchical clustering, and principal component analysis (PCA). Cluster analysis clustered all genotypes into five different groups. The D² statistics confirmed maximum diversity of cluster-V genotypes against genotypes of cluster-IV regarding single kernel characteristics, whereas cluster-II genotypes revealed maximum diversity against cluster-III genotypes relating to grain nutritional profile. The contribution of PC-I regarding single kernel characteristics toward variability was highest (48.58%) and revealed positive factor loadings for kernel weight, kernel diameter, and kernel moisture, while the contribution of PC-I with respect to grain nutritional profile toward variability was highest (59.76%) and showed positive factor loadings for moisture and starch content. Varieties having good quality attributes can be combined by breeders via various breeding methods with the aim of developing high quality wheat in the future.

Application of X-ray computed tomography to analyze the structure of sorghum grain

BACKGROUND

The structural characteristics of whole sorghum kernels are known to affect end-use quality, but traditional evaluation of this structure is two-dimensional (i.e., cross section of a kernel). Current technology offers the potential to consider three-dimensional structural characteristics of grain. X-ray computed tomography (CT) presents one such opportunity to nondestructively extract quantitative data from grain caryopses which can then be related to end-use quality.

RESULTS

Phenotypic measurements were extracted from CT scans of grain sorghum caryopses. Extensive phenotypic variation was found for embryo volume, endosperm hardness, endosperm texture, endosperm volume, pericarp volume, and kernel volume. CT derived estimates were strongly correlated with ground truth measurements enabling the identification of genotypes with superior structural characteristics.

CONCLUSIONS

Presented herein is a phenotyping pipeline developed to quantify three-dimensional structural characteristics from grain sorghum caryopses which increases the throughput efficiency of previously difficult to measure traits. Adaptation of this workflow to other small-seeded crops is possible providing new and unique opportunities for scientists to study grain in a nondestructive manner which will ultimately lead to improvements end-use quality.

Impacts of Fungal Stalk Rot Pathogens on Physicochemical Properties of Sorghum Grain

Stalk rot diseases are among the most ubiquitous and damaging fungal diseases of sorghum (Sorghum bicolor (L.) Moench) worldwide. Although reports of quantitative yield losses to stalk rots are available, the impact of stalk rot on grain quality attributes is unknown. This study was conducted to test whether stalk rot diseases could affect grain mineral (N, P, K; Ca, Mg, Cu, Fe, Mn, and Zn) and macronutrient (protein, fat, and starch) content, ash content, and physical traits (unit grain weight, hardness, and diameter). A field experiment was conducted in 2013 and 2014 with four sorghum genotypes (two hybrids and two lines). Plants from each genotype were inoculated with four stalk rot pathogens (Fusarium andiyazi, F. proliferatum, F. thapsinum, and Macrophomina phaseolina) and mock-inoculated with phosphate-buffered saline (control). Grains collected from infected and control plants were analyzed for macronutrient and ash content using near-infrared reflectance spectroscopy, grain hardness and diameter using the single-kernel characterization system, and mineral content using the Rapid Flow Analyzer (Model RFA-300 for N) and inductively coupled plasma spectrometer (for P, K, Ca, Mg, Cu, Fe, Mn, and Zn). Although stalk rot pathogens significantly reduced unit grain weight, they did not significantly affect grain hardness and diameter and, therefore, may not affect milling quality. Pathogens significantly reduced all macronutrient and most mineral contents across genotypes and environments on a per-unit-grain basis, except N and Mg, which were affected in a genotype- and environment-specific manner, and Fe, which was not significantly affected. Most minerals tested were significantly and negatively correlated with disease severity (lesion length) and total grain weight per panicle. The hybrid tested (Pioneer 84G62) exhibited reduced mineral and macronutritional changes after stalk rot infection, providing insights into the possibility of producing high-yielding, nutritionally stable hybrids under stalk rot disease pressure through dedicated breeding efforts.

Effect of nitrogen fertilization and cover cropping systems on sorghum grain characteristics

Cover crop treatments and nitrogen (N) fertilization rates were investigated for their impact on sorghum grain quality attributes. Sorghum was planted in field plots treated with differing cover cropping systems and fertilization rates. The size (weight and diameter) and hardness of the kernels were influenced by both the cover crop and N rates. The protein content increased as the N rate increased and also with the addition of cover crops to the system. The protein digestibility values and starch granule size distributions were not affected by N rate or the cover cropping treatments. Soil properties were tested to determine relationships with grain quality attributes. The utilization of cover crops appears to increase the protein content without causing a deleterious effect on protein digestibility. The end-product quality is not hampered by the use of beneficial cropping systems necessary for sustainable agriculture.

Variability in tannin content, chemistry and activity in a diverse group of tannin containing sorghum cultivars

BACKGROUND

Tannins are large polyphenolic polymers and are known to bind proteins, limiting their digestibility, but are also excellent antioxidants. Numerous studies investigating the functional properties of sorghum tannin have been conducted by comparing grain samples from different sorghum lines without considering the other intrinsic characteristics of the grain. The purpose of this study was to remove the confounding intrinsic factors present in the endosperm so the effect of the tannins could be evaluated utilizing a unique decortication/reconstitution procedure.

RESULTS

The tannin content of the 14 cultivars tested ranged from 2.3 to 67.2 catechin equivalents. The bran fractions were studied for their impact on protein binding and antioxidant capacity. Protein digestibility by pepsin ranged from 8% to 58% at the highest tannin level addition. Protein binding ranged from 3.11 to 16.33 g blue bovine serum albumin kg⁻¹ bran. Antioxidant capacity ranged from 81.33 to 1122.54 µmol Trolox equivalents g⁻¹ bran. High-performance size-exclusion chromatography detailed molecular size distributions of the tannin polymers and relationship to tannin functionality.

CONCLUSION

The tannin content and composition play a significant role in determining tannin functionality. These differences will allow for selections of high-tannin sorghums with consideration of the biological activities of the tannins.

Characterization of polymeric proteins from vitreous and floury sorghum endosperm

Differences in protein content and composition between vitreous and floury endosperm were investigated using a number of different techniques. Differences in protein cross-linking between vitreous and floury endosperm were investigated using differential solubility, size exclusion chromatography (SEC), and analysis of sulfhydryl content and composition. Vitreous endosperm was found to have higher levels of total protein and kafirins, but floury endosperm had a higher proportion of gamma-kafirins than the vitreous. Floury endosperm was found to have higher levels of SDS-soluble proteins than SDS-insoluble proteins extracted using sonication than vitreous endosperm. Conversely, vitreous endosperm had a greater proportion of the insoluble proteins. SEC analysis of the polymeric proteins revealed that the insoluble proteins had more polymeric proteins than did the soluble proteins, indicating greater cross-linking and a larger Mw distribution. Vitreous endosperm was also found to have a greater percentage (i.e., a higher ratio of disulfide to total sulfhydryls) of disulfide bonds than floury endosperm. These results show that the proteins in vitreous endosperm have a higher degree of cross-linking and a greater Mw distribution than those found in floury endosperm.