Hao Luo

Chickpea has become an increasingly popular healthy food worldwide. Aluminum (Al) toxicity is a major hurdle for chickpea cultivation and yield improvement in acidic soils. However, the genetic mechanism of Al-tolerance in chickpea remains poorly understood. Here, we performed a large-scale hydroponics screening and SNP chip array genotyping of 1154 diverse chickpea accessions. Root lengths after 6 days cultivation under hydroponics in control (T0: pH 4.2) and Al treatment (T1: pH4.2, 15/20 μM Al3+) were measured. Root tolerance index (RTI = T1/T0) ranking revealed significant variations in chickpea Al-tolerance, with common Australian chickpea cultivars positioned in the low to medium range. Genome-wide association analyses revealed eight QTLs on chromosomes ca1 (CaAlt1-1), ca3 (CaAlt3-1), ca4 (CaAlt4-1, CaAlt4-2), ca5(CaAlt5-1), ca6 (CaAlt6-1), and ca7 (CaAlt7-1, CaAlt7-2) associated with T1, implying a multigenic genetic basis for Al-tolerance in chickpea. Specifically, CaAlt7-2 was associated with both T1 and RTI, whilst CaAlt4-2 was detected for T1 uniquely in the HatTrick x CudiB22C population. Al- tolerant and sensitive haplotypes for the identified QTLs were also identified. Organic acid transporter genes CaMATE2, CaMATE4, and CaALMT1 were found in proximal genomic regions to CaAlt7-2, CaAlt4-1, and CaAlt6-1, respectively. Further qRT-PCR in parental chickpea lines (HatTrick, Slasher, Gunas, CudiB) confirmed that CaMATE2 and CaMATE4 were strongly induced upon Al treatment. Interestingly, CaMATE2 was preferentially expressed in the upper part of the root, whilst CaMATE4 preferentially in the root tips, implying a potential complementary role in Al resistance. Their direct roles in Al tolerance and the potential alternative candidate genes near the QTLs require further investigation. This first report of QTLs on Al-tolerance in chickpea has substantially advanced our understanding of the genetic basis of Al tolerance in chickpea and will facilitate the rapid breeding of Al-tolerant chickpea cultivars for previously un-accessible acidic soils.

Background
Grain colour is an important quality trait affecting the market value and consumer preference. Chickpeas with black-coloured seed coat is known for their beneficial high antioxidant and fibber content, yet the underlying molecular basis remains poorly understood.

Results
Here, we examined the grain colour trait of a panel of 261 diverse desi chickpea (Cicer arietinum) accessions and specially characterized the development of the black seed coat. We showed that the black colouration emerged on embryo tips at 30 days after flowering (DAF) and expanded to whole grain at 35 DAF. Genome-wide association analyses revealed a single major genetic locus CaBlk3-1 on chromosome Ca3 controlling black seed coat. Candidate gene screening within 0.5 Mb upstream and downstream of CaBlk3-1 identified a single MYB-encoding gene CaMYB114 related to anthocyanin biosynthesis. Phylogeny analyses showed that CaMYB114 was clustered with Arabidopsis MYB90, MYB113, MYB114, consistent with their role in anthocyanin production. Subsequent qRT-PCR analyses suggested that CaMYB114 was abundantly transcribed in black genotypes but weakly in the brown genotypes at 35 DAF, closely linked with black colour development. Genetic variation analyses of CaMYB114 identified a 12-bp deletion containing a GAGA motif in the 5UTR region of black chickpea genotype. A gene-specific marker targeting this deletion was developed to validate its link with the black seed coat in a larger chickpea germplasm collection.

Conclusions
We identified a single major QTL and the underlying candidate gene CaMYB114 closely associated with the black seed coat trait in chickpea. Our study has greatly improved our understanding of the genetic basis of chickpea black seed and will unlock the potential for breeding new chickpeas with desired grain colour to meet various market requirements.

Agriculture is a major contributor to global environmental challenges and is highly vulnerable to climate change. High-technology greenhouse farming provides efficient, secure and climate-resilient food production but costs significant energy to operate. We designed and constructed a greenhouse with high-transparency photovoltaic windows used as roof- and wall-mounted components of building envelope and demonstrated its significant potential to improve the sustainability of greenhouse farming. This innovative structure reduced energy consumption by 57% and water usage by 29% in research-scale greenhouse production. We showed that several crops commonly produced in greenhouses exhibited no yield loss when grown in solar greenhouses, including tomato, snow pea, spinach mustard, dwarf bean, bell pepper and lettuce. Due to a limitation in the experimental design, solar windows were not fully installed on the greenhouse, which led to an underestimation of the potential energy savings. A computing model showed that a fully glazed solar greenhouse has the potential to offset up to 100% of the energy consumption in worldwide locations by using adaptable and efficient temperature control techniques, thereby potentially enabling completely self-sustainable greenhouse farming on a global scale. The potential of self-sustainable greenhouse farming could be further enhanced by refining its wavelength-selective transmittance and using genetic manipulation to engineer crops that thrive in the solar greenhouse environment. The solar greenhouse technology represents significant opportunities to make substantial progress towards achieving net-zero emissions in global food systems by 2050.

Divergent selection of populations in contrasting environments leads to functional genomic divergence. However, the genomic architecture underlying heterogeneous genomic differentiation remains poorly understood. Here, we de novo assembled two high-quality wild barley (Hordeum spontaneum K. Koch) genomes and examined genomic differentiation and gene expression patterns under abiotic stress in two populations. These two populations had a shared ancestry and originated in close geographic proximity but experienced different selective pressures due to their contrasting micro-environments. We identified structural variants that may have played significant roles in affecting genes potentially associated with well-differentiated phenotypes such as flowering time and drought response between two wild barley genomes. Among them, a 29-bp insertion into the promoter region formed a cis-regulatory element in the HvWRKY45 gene, which may contribute to enhanced tolerance to drought. A single SNP mutation in the promoter region may influence HvCO5 expression and be putatively linked to local flowering time adaptation. We also revealed significant genomic differentiation between the two populations with ongoing gene flow. Our results indicate that SNPs and small SVs link to genetic differentiation at the gene level through local adaptation and are maintained through divergent selection. In contrast, large chromosome inversions may have shaped the heterogeneous pattern of genomic differentiation along the chromosomes by suppressing chromosome recombination and gene flow. Our research offers novel insights into the genomic basis underlying local adaptation and provides valuable resources for the genetic improvement of cultivated barley.

Pecan (Carya illinoinensis) is a world-famous nut tree widely cultivated in China. Quanjiao County, located in Anhui Province, is reputed to be the capital of pecan production in China. Since 2019, typical scab symptoms were observed on most pecan cultivars in orchards located in the regions of Quanjiao (32°5′7.08″N, 118°16′2.91″E). In April 2019, dark brown to black lesions of scab were observed on abaxial and adaxial surfaces of the lamina, and were often associated with the veins or midrib. In July, small, brownish, circular lesions 1 to 2 mm in diameter were observed at the end of stems and shoulder of the fruit. In surveyed orchards, disease incidence on leaves reached more than 35%. According to the number of infected nut clusters, disease incidence ranged from 40 to 60% on the infected fruits. Using a sterilized scalpel, conidia were scraped from the surface of a single lesion from the infected leaves or fruits, and a dilute spore suspension was prepared in sterile distilled water, of which 100 μl was spread on 1% water agar plate (Bock et al. 2014). The conidia were incubated at 25°C for 48 h under fluorescent lights with a 12-h photoperiod. Single germinated conidia were selected and transferred into potato dextrose agar (PDA) plate to obtain monospore isolates. From 2019 to 2020, more than 20 isolates were obtained from the infected leaves and fruits. After incubation at 24°C for 6 weeks in darkness on PDA, the colonies were gray-black with circular morphology and floccose texture, which were consistent with the characteristics of Venturia effusa described previously (Gottwald 1982). The conidia were pyriform to ellipsoid, zero to one septate, smooth, attenuated toward apex and base, base truncate, pale brown, and 10.08 to 18.14 × 4.86 to 9.56 μm (n = 50) in size. To further identify the isolates, the regions of internal transcribed spacer (ITS), beta-tubulin 2 (TUB2), and translation elongation factor 1 alpha (EF1-a) were amplified and sequenced from genomic DNA for the three representative isolates (AH-81 and AH-82 from the infected leaves, and AH-41 from the infected fruits), respectively (Bensch et al. 2006; White et al. 1990; Young et al. 2018). Sequences of them were deposited in GenBank under nos. OP199056 to OP199058 (ITS), OP566581 to OP566583 (TUB2), and OP566578 to OP566580 (EF1-a). Multilocus phylogenetic analysis revealed that three isolates and V. effusa were clustered in the same clade, indicating high genetic similarity between these organisms. Their morphological and molecular characteristics were consistent with those for V. effusa. The pathogenicity of three isolates were tested on 2-year-old container-grown pecan seedlings, which were grown in the nursery. The conidial suspension with a concentration of 5 × 105 conidia/ml was sprayed evenly on the surface of leaves of a healthy pecan seedling, and each isolate inoculated four pecan seedlings. The pathogenicity experiment was repeated three times. Plants inoculated with sterile water were used as negative controls. Inoculated plants were enclosed in plastic bags for 2 days and kept in the nursery greenhouse. Four weeks after inoculation, a similar symptom of scab was observed on leaves of cultivar Mahan, and V. effusa was isolated from all inoculated leaves by single-spore isolation, whereas no symptoms were observed on the control plants. To our knowledge, this is the first report of V. effusa as a scab pathogen on pecan in Anhui Province of China and underscores the need for monitoring this disease and developing disease control strategies to prevent severe reduction in the value of fruit.

Australia has a reputation for producing a reliable supply of high-quality barley in a contaminant-free climate. As a result, Australian barley is highly sought after by malting, brewing, distilling, and feed industries worldwide. Barley is traded as a variety-specific commodity on the international market for food, brewing and distilling end-use, as the intrinsic quality of the variety determines its market value. Manual identification of barley varieties by the naked eye is challenging and time-consuming for all stakeholders, including growers, grain handlers and traders. Current industrial methods for identifying barley varieties include molecular protein weights or DNA based technology, which are not only time-consuming and costly but need specific laboratory equipment. On grain receival, there is a need for efficient and low-cost solutions for barley classification to ensure accurate and effective variety segregation. This paper proposes an efficient deep learning-based technique that can classify barley varieties from RGB images. Our proposed technique takes only four milliseconds to classify an RGB image. The proposed technique outperforms the baseline method and achieves a barley classification accuracy of 94% across 14 commercial barley varieties (some highly genetically related).

Breeding crop cultivars with optimal value across multiple traits has been a challenge, as traits may negatively correlate due to pleiotropy or genetic linkage. For example, grain yield and grain protein content correlate negatively with each other in cereal crops. Future crop breeding needs to be based on practical yet accurate evaluation and effective selection of beneficial trait to retain genes with the best agronomic score for multiple traits. Here, we test the framework of whole-system-based approach using structural equation modelling (SEM) to investigate how one trait affects others to guide the optimal selection of a combination of agronomically important traits. Using ten traits and genome-wide SNP profiles from a worldwide barley panel and SEM analysis, we revealed a network of interacting traits, in which tiller number contributes positively to both grain yield and protein content; we further identified common genetic factors affecting multiple traits in the network of interaction. Our method demonstrates an efficient way to identify genetically correlating traits and underlying pleiotropic genetic factors and provides an effective proxy for multi-trait selection within a whole-system framework that considers the joint genetic architecture of multiple interacting traits in crop breeding. Our findings suggest the promise of a whole-system approach to overcome challenges such as the negative correlation of grain yield and protein content to facilitating quantitative and objective breeding decisions in future crop breeding.

Sucrose content is a crucial indicator of quality and flavor in peanut seed, and there is a lack of clarity on the molecular basis of sucrose metabolism in peanut seed. In this context, we performed a comprehensive comparative transcriptome study on the samples collected at seven seed development stages between a high-sucrose content variety (ICG 12625) and a low-sucrose content variety (Zhonghua 10). The transcriptome analysis identified a total of 8334 genes exhibiting significantly different abundances between the high- and low-sucrose varieties. We identified 28 differentially expressed genes (DEGs) involved in sucrose metabolism in peanut and 12 of these encoded sugars will eventually be exported transporters (SWEETs). The remaining 16 genes encoded enzymes, such as cell wall invertase (CWIN), vacuolar invertase (VIN), cytoplasmic invertase (CIN), cytosolic fructose-bisphosphate aldolase (FBA), cytosolic fructose-1,6-bisphosphate phosphatase (FBP), sucrose synthase (SUS), cytosolic phosphoglucose isomerase (PGI), hexokinase (HK), and sucrose-phosphate phosphatase (SPP). The weighted gene co-expression network analysis (WGCNA) identified seven genes encoding key enzymes (CIN, FBA, FBP, HK, and SPP), three SWEET genes, and 90 transcription factors (TFs) showing a high correlation with sucrose content. Furthermore, upon validation, six of these genes were successfully verified as exhibiting higher expression in high-sucrose recombinant inbred lines (RILs). Our study suggested the key roles of the high expression of SWEETs and enzymes in sucrose synthesis making the genotype ICG 12625 sucrose-rich. This study also provided insights into the molecular basis of sucrose metabolism during seed development and facilitated exploring key candidate genes and molecular breeding for sucrose content in peanuts.

Background Drought is projected to become more frequent and severe in a changing climate, which requires deep sowing of crop seeds to reach soil moisture. Coleoptile length is a key agronomic trait in cereal crops such as barley, as long coleoptiles are linked to drought tolerance and improved seedling establishment under early water-limited growing conditions. Results In this study, we detected large genetic variation in a panel of 328 diverse barley (Hordeum vulgare L.) accessions. To understand the overall genetic basis of barley coleoptile length, all accessions were germinated in the dark and phenotyped for coleoptile length after 2 weeks. The investigated barleys had significant variation for coleoptile length. We then conducted genome-wide association studies (GWASs) with more than 30,000 molecular markers and identified 8 genes and 12 intergenic loci significantly associated with coleoptile length in our barley panel. The Squamosa promoter-binding-like protein 3 gene (SPL3) on chromosome 6H was identified as a major candidate gene. The missense variant on the second exon changed serine to alanine in the conserved SBP domain, which likely impacted its DNA-binding activity. Conclusion This study provides genetic loci for seedling coleoptile length along with candidate genes for future potential incorporation in breeding programmes to enhance early vigour and yield potential in water-limited environments.

Protein Z is a major component in beer foam. Two-dimensional electrophoresis was used to analyze wort proteins of two Australian (Buloke and Commander) and two Canadian (CDC Meredith and Bentley) varieties. The Canadian barley contained more abundant proteins from MW 40–45 kDa (pI 5 to 7). These proteins were identified as either protein Z4 or protein Z7 using liquid chromatography–mass spectrometry. Full-length gene of protein Z4 and Z7 were sequenced from Canadian and Australian barleys. Sequence differences were identified in the coding region and upstream regions of the two genes, resulting in protein sequence and expression variations. Molecular markers were designed according to the indels in the upstream regions of protein Z4 and Z7 genes. These markers were highly correlated to wort protein Z content in Canadian and Australian varieties. The Canadian barleys contained ‘high level’ genotypes for protein Z4 and Z7 while most Australian barleys had ‘low level’ genotypes for protein Z4, Z7 or both. The markers identified in this study provide a valuable tool for the selection of protein Z alleles in marker-assisted breeding. Total protein Z content was assessed using different steeping conditions, and increasing air-rest time increased protein Z content in 15 varieties.