Resequencing of 145 Landmark Cultivars Reveals Asymmetric Sub-genome Selection and Strong Founder Genotype Effects on Wheat Breeding in China

Identifying genotypes with a greater ability to absorb nitrogen (N) may be important to reducing N loss in the environment and improving the sustainability of agricultural systems. This study extends the knowledge of variability among wheat genotypes in terms of morphological or physiological root traits, N uptake under conditions of low soil N availability, and in the amount and rapidity of the use of N supplied with fertilizer. Nine genotypes of durum wheat were chosen for their different morpho-phenological characteristics and year of their release. The isotopic tracer 15N was used to measure the fertilizer N uptake efficiency. The results show that durum wheat breeding did not have univocal effects on the characteristics of the root system (weight, length, specific root length, etc.) or N uptake capacity. The differences in N uptake among the studied genotypes when grown in conditions of low N availability appear to be related more to differences in uptake efficiency per unit of weight and length of the root system than to differences in the morphological root traits. The differences among the genotypes in the speed and the ability to take advantage of the greater N availability, determined by N fertilization, appear to a certain extent to be related to the development of the root system and the photosynthesizing area. This study highlights some variability within the species in terms of the development, distribution, and efficiency of the root system, which suggests that there may be sufficient grounds for improving these traits with positive effects in terms of adaptability to difficult environments and resilience to climate change.

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Automatic Evaluation of Wheat Resistance to Fusarium Head Blight Using Dual Mask-RCNN Deep Learning Frameworks in Computer Vision

Remote Sensing ◽

10.3390/rs13010026 ◽

2020 ◽

Vol 13 (1) ◽

pp. 26

Author(s):

Wen-Hao Su ◽

Jiajing Zhang ◽

Ce Yang ◽

Rae Page ◽

Tamas Szinyei ◽

...

Keyword(s):

Fusarium Head Blight ◽

Ground Truth ◽

Wheat Breeding ◽

Head Blight ◽

Detection Rates ◽

Ground Truth Data ◽

Resistant Cultivars ◽

Feature Pyramid ◽

Rater Error ◽

Wheat Lines

In many regions of the world, wheat is vulnerable to severe yield and quality losses from the fungus disease of Fusarium head blight (FHB). The development of resistant cultivars is one means of ameliorating the devastating effects of this disease, but the breeding process requires the evaluation of hundreds of lines each year for reaction to the disease. These field evaluations are laborious, expensive, time-consuming, and are prone to rater error. A phenotyping cart that can quickly capture images of the spikes of wheat lines and their level of FHB infection would greatly benefit wheat breeding programs. In this study, mask region convolutional neural network (Mask-RCNN) allowed for reliable identification of the symptom location and the disease severity of wheat spikes. Within a wheat line planted in the field, color images of individual wheat spikes and their corresponding diseased areas were labeled and segmented into sub-images. Images with annotated spikes and sub-images of individual spikes with labeled diseased areas were used as ground truth data to train Mask-RCNN models for automatic image segmentation of wheat spikes and FHB diseased areas, respectively. The feature pyramid network (FPN) based on ResNet-101 network was used as the backbone of Mask-RCNN for constructing the feature pyramid and extracting features. After generating mask images of wheat spikes from full-size images, Mask-RCNN was performed to predict diseased areas on each individual spike. This protocol enabled the rapid recognition of wheat spikes and diseased areas with the detection rates of 77.76% and 98.81%, respectively. The prediction accuracy of 77.19% was achieved by calculating the ratio of the wheat FHB severity value of prediction over ground truth. This study demonstrates the feasibility of rapidly determining levels of FHB in wheat spikes, which will greatly facilitate the breeding of resistant cultivars.

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Recent advances in CRISPR/Cas9 and applications for wheat functional genomics and breeding

aBIOTECH ◽

10.1007/s42994-021-00042-5 ◽

2021 ◽

Author(s):

Jun Li ◽

Yan Li ◽

Ligeng Ma

Keyword(s):

Functional Genomics ◽

Genome Editing ◽

Functional Annotation ◽

Genome Engineering ◽

Agronomic Traits ◽

Wheat Breeding ◽

Breeding Programs ◽

Base Editing ◽

The World ◽

World Food Security

AbstractCommon wheat (Triticum aestivum L.) is one of the three major food crops in the world; thus, wheat breeding programs are important for world food security. Characterizing the genes that control important agronomic traits and finding new ways to alter them are necessary to improve wheat breeding. Functional genomics and breeding in polyploid wheat has been greatly accelerated by the advent of several powerful tools, especially CRISPR/Cas9 genome editing technology, which allows multiplex genome engineering. Here, we describe the development of CRISPR/Cas9, which has revolutionized the field of genome editing. In addition, we emphasize technological breakthroughs (e.g., base editing and prime editing) based on CRISPR/Cas9. We also summarize recent applications and advances in the functional annotation and breeding of wheat, and we introduce the production of CRISPR-edited DNA-free wheat. Combined with other achievements, CRISPR and CRISPR-based genome editing will speed progress in wheat biology and promote sustainable agriculture.

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Evaluation of a Novel Molecular Marker Associated with the Tan Spot Disease Response in Wheat

Agriculture ◽

10.3390/agriculture11060513 ◽

2021 ◽

Vol 11 (6) ◽

pp. 513

Author(s):

Pao Theen See ◽

Caroline S. Moffat

Keyword(s):

Molecular Marker ◽

Hexaploid Wheat ◽

Wheat Breeding ◽

Tan Spot ◽

Growth Stages ◽

Disease Score ◽

Wheat Varieties ◽

Disease Response ◽

Spot Disease ◽

Tan Spot Disease

After nearly 40 years of DNA molecular marker development in plant breeding, the wheat research community has amassed an extensive collection of molecular markers which have been widely and successfully used for selection of agronomic, physiological and disease resistance traits in wheat breeding programs. Tan spot is a major fungal disease of wheat and a significant global economic challenge and is caused by the necrotrophic fungal pathogen Pyrenophora tritici-repentis (Ptr). Here, the potential for using a PCR-based marker (Ta1AS3422) present on the short arm of wheat chromosome 1A, was evaluated for effectiveness in distinguishing tan spot disease susceptibility. The marker was initially screened against 40 commercial Australian hexaploid wheat varieties, and those that amplified the marker had an overall lower disease score (2.8 ± 0.7 for seedlings and 2.4 ± 0.4 for plants at the tillering stage), compared to those lacking the marker which exhibited a higher disease score (3.6 ± 0.8 for both growth stages). The potential of Ta1AS3422 as a marker for the tan spot disease response was further assessed against a panel of 100 commercial Australian hexaploid wheat varieties. A significant association was observed between marker absence/presence and tan spot disease rating (Pearson’s chi-squared test, χ2 (6) = 20.53, p = 0.002), with absence of Ta1AS3422 associated with susceptibility. This simple and cost-effective PCR-based marker may be useful for varietal improvement against tan spot, although further work is required to validate its effectiveness.

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Genetic architecture underlying the expression of eight α-amylase trypsin inhibitors

Theoretical and Applied Genetics ◽

10.1007/s00122-021-03906-y ◽

2021 ◽

Author(s):

Khaoula EL Hassouni ◽

Malte Sielaff ◽

Valentina Curella ◽

Manjusha Neerukonda ◽

Willmar Leiser ◽

...

Keyword(s):

Genetic Architecture ◽

Intestinal Inflammation ◽

Wheat Breeding ◽

Trypsin Inhibitors ◽

Potential Candidate ◽

Lipid Transfer ◽

Wheat Cultivars ◽

Genome Wide ◽

Close Physical Proximity ◽

Major Qtl

Abstract Key message Wheat cultivars largely differ in the content and composition of ATI proteins, but heritability was quite low for six out of eight ATIs. The genetic architecture of ATI proteins is built up of few major and numerous small effect QTL. Abstract Amylase trypsin inhibitors (ATIs) are important allergens in baker’s asthma and suspected triggers of non-celiac wheat sensitivity (NCWS) inducing intestinal and extra-intestinal inflammation. As studies on the expression and genetic architecture of ATI proteins in wheat are lacking, we evaluated 149 European old and modern bread wheat cultivars grown at three different field locations for their content of eight ATI proteins. Large differences in the content and composition of ATIs in the different cultivars were identified ranging from 3.76 pmol for ATI CM2 to 80.4 pmol for ATI 0.19, with up to 2.5-fold variation in CM-type and up to sixfold variation in mono/dimeric ATIs. Generally, heritability estimates were low except for ATI 0.28 and ATI CM2. ATI protein content showed a low correlation with quality traits commonly analyzed in wheat breeding. Similarly, no trends were found regarding ATI content in wheat cultivars originating from numerous countries and decades of breeding history. Genome-wide association mapping revealed a complex genetic architecture built of many small, few medium and two major quantitative trait loci (QTL). The major QTL were located on chromosomes 3B for ATI 0.19-like and 6B for ATI 0.28, explaining 70.6 and 68.7% of the genotypic variance, respectively. Within close physical proximity to the medium and major QTL, we identified eight potential candidate genes on the wheat reference genome encoding structurally related lipid transfer proteins. Consequently, selection and breeding of wheat cultivars with low ATI protein amounts appear difficult requiring other strategies to reduce ATI content in wheat products.

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Unravelling the hidden inter and intra-varietal diversity of durum wheat commercial varieties used in Portugal

Plant Genetic Resources ◽

10.1017/s1479262119000133 ◽

2019 ◽

Vol 17 (04) ◽

pp. 386-389

Author(s):

Miguel Bento ◽

Sónia Gomes Pereira ◽

Wanda Viegas ◽

Manuela Silva

Keyword(s):

Durum Wheat ◽

Repetitive Sequences ◽

Inter Simple Sequence Repeat ◽

Wheat Breeding ◽

Genomic Diversity ◽

Varietal Diversity ◽

Wheat Varieties ◽

Coding Sequences ◽

Coding Regions ◽

High Level

AbstractAssessing durum wheat genomic diversity is crucial in a changing environmental particularly in the Mediterranean region where it is largely used to produce pasta. Durum wheat varieties cultivated in Portugal and previously assessed regarding thermotolerance ability were screened for the variability of coding sequences associated with technological traits and repetitive sequences. As expected, reduced variability was observed regarding low molecular weight glutenin subunits (LMW-GS) but a specific LMW-GS allelic form associated with improved pasta-making characteristics was absent in one variety. Contrastingly, molecular markers targeting repetitive elements like microsatellites and retrotransposons – Inter Simple Sequence Repeat (ISSR) and Inter Retrotransposons Amplified Polymorphism (IRAP) – disclosed significant inter and intra-varietal diversity. This high level of polymorphism was revealed by the 20 distinct ISSR/IRAP concatenated profiles observed among the 23 individuals analysed. Interestingly, median joining networks and PCoA analysis grouped individuals of the same variety and clustered varieties accordingly with geographical origin. Globally, this work demonstrates that durum wheat breeding strategies induced selection pressure for some relevant coding sequences while maintaining high levels of genomic variability in non-coding regions enriched in repetitive sequences.

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