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Germplasm collections hold valuable allelic diversity for crop improvement and genetic mapping of complex traits. To gain access to the genetic diversity within the USDA National Small Grain Collection (NSGC), we developed the Barley Recombinant Inbred Diverse Germplasm Population (BRIDG6), a six-row spring barley multiparent population (MPP) with 88 cultivated accessions crossed to a common parent (Rasmusson). The parents were randomly selected from a core subset of the NSGC that represents the genetic diversity of landrace and breeding accessions. In total, we generated 6160 F5 recombinant inbred lines (RILs), with an average of 69 and a range of 37–168 RILs per family, that were genotyped with 7773 SNPs, with an average of 3889 SNPs segregating per family. We detected 23 quantitative trait loci (QTL) associated with flowering time with five QTL found coincident with previously described flowering time genes. A major QTL was detected near the flowering time gene, HvPpd-H1 which affects photoperiod. Haplotype-based analysis of HvPpd-H1 identified private alleles to families of Asian origin conferring both positive and negative effects, providing the first observation of flowering time-related alleles private to Asian accessions. We evaluated several subsampling strategies to determine the effect of sample size on the power of QTL detection, and found that, for flowering time in barley, a sample size >50 families or 3000 individuals results in the highest power for QTL detection. This MPP will be useful for uncovering large and small effect QTL for traits of interest, and identifying and utilizing valuable alleles from the NSGC for barley improvement.

Grain filling is an importantly developmental process which is associated with the yield and quality of foxtail millet (Setaria italic L.). However, the molecular mechanisms of grain filling are rarely reported in foxtail millet. In our study, RNA-seq was performed to investigate the transcriptional dynamics and identify the key genes involved in grain filling in foxtail millet at five different developmental stages. A total of 11,399 differentially expressed genes (DEGs), including 902 transcription factors (TFs), were identified. Certain important genes involved in grain filling were discovered through a function annotation and temporal expression patterns analysis. These genes included genes associated with starch biosynthesis, cell-wall invertases, hormone signal transduction, and polyamine metabolism pathways. The expression levels of seven randomly selected DEGs were validated by a quantitative real-time polymerase chain reaction (qRT-PCR). This study provides the first insight into the changes in the gene expression of grain filling at different developmental stages in foxtail millet. These results could help understand the complex molecular mechanisms of the panicle formation in foxtail millet and other cereal crops.

Salinity is a major abiotic stress affecting cereal production. Thus, tritipyrum (x. Tritipyrum ), a potential novel salt-tolerant cereal, was introduced as an appropriate alternative for cereal production. The purposes of this study were to evaluate agronomic traits, yield, and yield stability of eight primary tritipyrum lines, five promising triticale lines, and four bread wheat varieties and to screen a stable yielding line. The experiments were conducted in randomized complete block designs with three replicates in three locations during four growing seasons. Analysis of variance in each environment and Bartlett’s test for the variance homogeneity of experimental errors were made. Subsequently, separate experiments were analyzed as a combined experiment. The stability of grain yield was analyzed according to Eberhart and Russell’s regression method, environmental variance, Wrick’s ecovalance, Shokla’s stability variance, AMMI, and Tai methods. Genotype × environment interactions (GEI) and environments were significant for the agronomic traits. Stability analysis revealed that combined primary tritipyrum line (Ka/b)(Cr/b)-5 and triticale 4115, 4108, and M45 lines had good adaptability in all environments. The results of the AMMI3 model and pattern analysis showed that the new cereal, tritipyrum, had the most stable response in various environments. The tritipyrum line (Ka/b)(Cr/b)-5 had the best yield performance and general adaptability. Based on Tai’s method, the contribution of spike number to the stability of grain yield over different environments was higher than that of other yield components. Also, tritipyrum lines demonstrated higher stability compared with wheat and triticale. Totally, M45 triticale and tritipyrum (Ka/b)(Cr/b)-5 lines were the most stable genotypes with high grain yield. Complementary agronomic experiments may then release a new grain crop of triticale and a new pasture line of combined primary tritipyrum for grain and forage. Moreover, the combined tritipyrum line can be used in bread wheat breeding programs for producing salt-tolerant wheat cultivars.

Background The increasing temperatures due to climate change around the world poses a serious threat to sustainable crop production. The growing adverse effects of heat stress are putting global food security at great risk. Crop improvement for adaptation to increased temperatures is therefore of paramount importance. This study aims at assessing the effects of heat stress in relation to agro-morphological and physiological traits of six rice varieties. The study was carried out in the Township of Glazoué, a rice-growing area in Benin. The experiments were laid in randomized complete block design with three replications. Two types of stress were imposed: high-temperature stress in the dry season and optimal temperatures in the rainy season. The calculated mean values of morphological, physiological, and agronomic traits were used to estimate heritability, genetic advance, PCA, and correlation. Results The results showed that heat stress had a significant ( p  ≤ 0.01) influence on plant height, leaf length, number of tillers, number of internodes, days to flowering, and days to maturity, 1000-seed weight, and yield per plant. The heat stress had significantly delayed the flowering of all the varieties when compared to the controls. The highest values of 1000-seed weight (34. 67 g) were recorded for BRIZ-8B while the lowest (25.33 g) were recorded for NERICA-L20. The highest values for the genotypic coefficient of variation (43.05%) and phenotypic coefficient of variation (99.13%) were recorded for yield per plant under heat stress. The topmost broad-sense heritability was recorded for grain width (92.72%), followed by days to maturity (69.33%), days to flowering (68.50%), number of grains per panicle (57.35%), and yield (54.55%). Conclusions These results showed that BRIZ-8B and BRIZ-10B were the most tolerant to high temperature amongst the six varieties assessed and potentially could be recommended to farmers for production under high temperature and be used in breeding programs to improve heat tolerance in rice.

Maize ( Zea mays L.) is native to Mexico, in which wide genetic diversity can be found; however, maize is at risk of genetic erosion, and agroforestry systems (ASs) can be a strategy for conservation and sustainable use of this crop. The objective of this study was to evaluate the variation in the morpho-agronomic characteristics of three native maize races, Tuxpeño, Olotillo × Tuxpeño and Ratón × Tepecintle, cultivated in different AS in a tropical climate of Veracruz, Mexico, as well as its association with microclimatic conditions. In 2019, experiments were established in the localities La Gloria and La Luisa, Veracruz, where the three maize races are cultivated, in a randomized complete block design with three replications in a 3 × 4 factorial scheme (three native maize races and three AS arrrays, plus monoculture). Ten morpho-agronomic variables were recorded in each experiment and were analyzed by analysis of variance (ANOVA; Tukey’s post-hoc test, all p ≤ 0.05) and principal component analysis (PCA). Six morpho-agronomic characteristics showed significant differences for the race × system interaction. Consistently standing out both in the Myroxylon with 2.8 m × 2.0 arrays and in the monoculture was the Olotillo × Tuxpeño race, as there were no variations ( p ≥ 0.05) in 50% of its morpho-agronomic characteristics. The first three PCs explained 87.7% of the cumulative variance, determined by five variables of the ears, three of the grain and plant height, which were associated with temperature; therefore, the microclimatic conditions of the studied ASs are associated with the morpho-agronomic characteristics of the native maize races. The results show that ASs could be a strategy for the conservation and use of native corn germplasm and could allow the diversification of sustainable production for rural farmers.

Advances in genomics have expedited the improvement of several agriculturally important crops but similar efforts in wheat ( Triticum spp.) have been more challenging. This is largely owing to the size and complexity of the wheat genome 1 , and the lack of genome-assembly data for multiple wheat lines 2 , 3 . Here we generated ten chromosome pseudomolecule and five scaffold assemblies of hexaploid wheat to explore the genomic diversity among wheat lines from global breeding programs. Comparative analysis revealed extensive structural rearrangements, introgressions from wild relatives and differences in gene content resulting from complex breeding histories aimed at improving adaptation to diverse environments, grain yield and quality, and resistance to stresses 4 , 5 . We provide examples outlining the utility of these genomes, including a detailed multi-genome-derived nucleotide-binding leucine-rich repeat protein repertoire involved in disease resistance and the characterization of Sm1 6 , a gene associated with insect resistance. These genome assemblies will provide a basis for functional gene discovery and breeding to deliver the next generation of modern wheat cultivars. Comparison of multiple genome assemblies from wheat reveals extensive diversity that results from the complex breeding history of wheat and provides a basis for further potential improvements to this important food crop.

Modern green revolution varieties of wheat ( Triticum aestivum L.) confer semi-dwarf and lodging-resistant plant architecture owing to the Reduced height-B1b ( Rht-B1b ) and Rht-D1b alleles 1 . However, both Rht-B1b and Rht-D1b are gain-of-function mutant alleles encoding gibberellin signalling repressors that stably repress plant growth and negatively affect nitrogen-use efficiency and grain filling 2 – 5 . Therefore, the green revolution varieties of wheat harbouring Rht-B1b or Rht-D1b usually produce smaller grain and require higher nitrogen fertilizer inputs to maintain their grain yields. Here we describe a strategy to design semi-dwarf wheat varieties without the need for Rht-B1b or Rht-D1b alleles. We discovered that absence of Rht-B1 and ZnF-B (encoding a RING-type E3 ligase) through a natural deletion of a haploblock of about 500 kilobases shaped semi-dwarf plants with more compact plant architecture and substantially improved grain yield (up to 15.2%) in field trials. Further genetic analysis confirmed that the deletion of ZnF-B induced the semi-dwarf trait in the absence of the Rht-B1b and Rht-D1b alleles through attenuating brassinosteroid (BR) perception. ZnF acts as a BR signalling activator to facilitate proteasomal destruction of the BR signalling repressor BRI1 kinase inhibitor 1 (TaBKI1), and loss of ZnF stabilizes TaBKI1 to block BR signalling transduction. Our findings not only identified a pivotal BR signalling modulator but also provided a creative strategy to design high-yield semi-dwarf wheat varieties by manipulating the BR signal pathway to sustain wheat production. A strategy that depends on attenuated brassinosteroid signalling is described for the design of semi-dwarf wheat varieties with improved grain yield compared with that of green revolution varieties.

Grain size is one of the key determinants of grain yield. Although a number of genes that control grain size in rice (Oryza sativa) have been identified, the overall regulatory networks behind this process remain poorly understood. Here, we report the map-based cloning and functional characterization of the quantitative trait locus GL6, which encodes a plant-specific plant AT-rich sequence- and zinc-binding transcription factor that regulates rice grain length and spikelet number. GL6 positively controls grain length by promoting cell proliferation in young panicles and grains. The null gl6 mutant possesses short grains, whereas overexpression of GL6 results in large grains and decreased grain number per panicle. We demonstrate that GL6 participates in RNA polymerase III transcription machinery by interacting with RNA polymerase III subunit C53 and transcription factor class C1 to regulate the expression of genes involved in rice grain development. Our findings reveal a further player involved in the regulation of rice grain size that may be exploited in future rice breeding.

Grain size is an important component trait of grain yield, which is frequently threatened by abiotic stress. However, little is known about how grain yield and abiotic stress tolerance are regulated. Here, we characterize GSA1 , a quantitative trait locus (QTL) regulating grain size and abiotic stress tolerance associated with metabolic flux redirection. GSA1 encodes a UDP-glucosyltransferase, which exhibits glucosyltransferase activity toward flavonoids and monolignols. GSA1 regulates grain size by modulating cell proliferation and expansion, which are regulated by flavonoid-mediated auxin levels and related gene expression. GSA1 is required for the redirection of metabolic flux from lignin biosynthesis to flavonoid biosynthesis under abiotic stress and the accumulation of flavonoid glycosides, which protect rice against abiotic stress. GSA1 overexpression results in larger grains and enhanced abiotic stress tolerance. Our findings provide insights into the regulation of grain size and abiotic stress tolerance associated with metabolic flux redirection and a potential means to improve crops. Increasing grain yield needs to be put in the context of environmental stress. Here, the authors reveal that a UDP-glucosyltransferase is associated with regulation of rice grain size, abiotic stress tolerance, flavonoid-mediated auxin signaling, and redirection of carbon flux to flavonoid glycosides synthesis.

Bin Han and colleagues present a genome-wide association analysis of grain size and shape in cultivated rice and identify a major locus for grain size encoding the transcription factor OsSPL13. They find that the large-grain allele in tropical japonica cultivars was introgressed from indica varieties during selection for improved grain yield. Although genetic diversity has a cardinal role in domestication, abundant natural allelic variations across the rice genome that cause agronomically important differences between diverse varieties have not been fully explored. Here we implement an approach integrating genome-wide association testing with functional analysis on grain size in a diverse rice population. We report that a major quantitative trait locus, GLW7 , encoding the plant-specific transcription factor OsSPL13, positively regulates cell size in the grain hull, resulting in enhanced rice grain length and yield. We determine that a tandem-repeat sequence in the 5′ UTR of OsSPL13 alters its expression by affecting transcription and translation and that high expression of OsSPL13 is associated with large grains in tropical japonica rice. Further analysis indicates that the large-grain allele of GLW7 in tropical japonica rice was introgressed from indica varieties under artificial selection. Our study demonstrates that new genes can be effectively identified on the basis of genome-wide association data.