Search

Due to evolutionary divergence, sorghum race populations exhibit vast genetic and morphological variations. A k-mer-based sorghum race sequence comparison identified the conserved k-mers of all sorghum race accessions and the race-specific genetic signatures identified the gene variability in 10,321 genes (PAVs). To understand the sorghum race structure, diversity and domestication, deep learning-based variant calling approach was employed in a set of genotypic data derived from a diverse panel of 272 sorghum accessions. The data resulted in 1.7 million high-quality genome-wide SNPs and identified selective signature (both positive and negative) regions through a genome-wide scan with different (iHS and XP-EHH) statistical methods. We discovered 2,370 genes associated with selection signatures including 179 selective sweep regions distributed over 10 chromosomes. Localization of these regions undergoing selective pressure with previously reported QTLs and genes revealed that the signatures of selection could be related to the domestication of important agronomic traits such as biomass and plant height. The developed k-mer signatures will be useful in the future to identify the sorghum race and SNP markers assist in plant breeding programs.

Sorghum (Sorghum bicolor L.) is a staple food crops in the arid and rainfed production ecologies. Sorghum plays a critical role in resilient farming and is projected as a smart crop to overcome the food and nutritional insecurity in the developing world. The development and characterisation of the sorghum pan-genome will provide insight into genome diversity and functionality, supporting sorghum improvement. We built a sorghum pan-genome using reference genomes as well as 354 genetically diverse sorghum accessions belonging to different races. We explored the structural and functional characteristics of the pan-genome and explain its utility in supporting genetic gain. The newly-developed pan-genome has a total of 35,719 genes, a core genome of 16,821 genes and an average of 32,795 genes in each cultivar. The variable genes are enriched with environment responsive genes and classify the sorghum accessions according to their race. We show that 53% of genes display presence-absence variation, and some of these variable genes are predicted to be functionally associated with drought adaptation traits. Using more than two million SNPs from the pan-genome, association analysis identified 398 SNPs significantly associated with important agronomic traits, of which, 92 were in genes. Drought gene expression analysis identified 1,788 genes that are functionally linked to different conditions, of which 79 were absent from the reference genome assembly. This study provides comprehensive genomic diversity resources in sorghum which can be used in genome assisted crop improvement.

Sorghum (Sorghum bicolorL.) is one of the most important food crops in the arid and rainfed production ecologies. It is a part of resilient farming and is projected as a smart crop to overcome the food and nutritional challenges in the developing world. The development and characterisation of the sorghum pan-genome will provide insight into genome diversity and functionality, supporting sorghum improvement. We built a sorghum pan-genome using reference genomes as well as 354 genetically diverse sorghum accessions belonging to different races. We explored the structural and functional characteristics of the pan-genome and explain its utility in supporting genetic gain. The newly-developed pan-genome has a total of 35,719 genes, a core genome of 16,821 genes and an average of 32,795 genes in each cultivar. The variable genes are enriched with environment responsive genes and classify the sorghum accessions according to their race. We show that 53% of genes display presence-absence variation, and some of these variable genes are predicted to be functionally associated with drought traits. Using more than two million SNPs from the pan-genome, association analysis identified 398 SNPs significantly associated with important agronomic traits, of which, 92 were in genes. Drought gene expression analysis identified 1,788 genes that are functionally linked to different conditions, of which 79 were absent from the reference genome assembly. This study provides comprehensive genomic diversity resources in sorghum which can be used in genome assisted crop improvement.

Stigma exsertion and panicle enclosure of male sterile lines are two key determinants of outcrossing in hybrid rice seed production. Based on 43,394 single nucleotide polymorphism markers, 217 cytoplasmic male sterile lines were assigned into two subpopulations and a mixed-group where the linkage disequilibrium decay distances varied from 975 to 2,690 kb. Genome-wide association studies (GWAS) were performed for stigma exsertion rate (SE), panicle enclosure rate (PE) and seed-setting rate (SSR). A total of 154 significant association signals (P

Impacts of population structure on the evaluation of genomic heritability and prediction were investigated and quantified using high-density markers in diverse panels in rice and maize. Population structure is an important factor affecting estimation of genomic heritability and assessment of genomic prediction in stratified populations. In this study, our first objective was to assess effects of population structure on estimations of genomic heritability using the diversity panels in rice and maize. Results indicate population structure explained 33 and 7.5% of genomic heritability for rice and maize, respectively, depending on traits, with the remaining heritability explained by within-subpopulation variation. Estimates of within-subpopulation heritability were higher than that derived from quantitative trait loci identified in genome-wide association studies, suggesting 65% improvement in genetic gains. The second objective was to evaluate effects of population structure on genomic prediction using cross-validation experiments. When population structure exists in both training and validation sets, correcting for population structure led to a significant decrease in accuracy with genomic prediction. In contrast, when prediction was limited to a specific subpopulation, population structure showed little effect on accuracy and within-subpopulation genetic variance dominated predictions. Finally, effects of genomic heritability on genomic prediction were investigated. Accuracies with genomic prediction increased with genomic heritability in both training and validation sets, with the former showing a slightly greater impact. In summary, our results suggest that the population structure contribution to genomic prediction varies based on prediction strategies, and is also affected by the genetic architectures of traits and populations. In practical breeding, these conclusions may be helpful to better understand and utilize the different genetic resources in genomic prediction.

Semidwarfism has been used extensively in row crops and horticulture to promote yield, reduce lodging, and improve harvest index, and it might have similar benefits for trees for short-rotation forestry or energy plantations, reclamation, phytoremediation, or other applications. We studied the effects of the dominant semidwarfism transgenes GA Insensitive (GAI) and Repressor of GAI-Like, which affect gibberellin (GA) action, and the GA catabolic gene, GA 2-oxidase, in nursery beds and in 2-year-old high-density stands of hybrid poplar (Populus tremula × Populus alba). Twenty-nine traits were analyzed, including measures of growth, morphology, and physiology. Endogenous GA levels were modified in most transgenic events; GA20 and GA8, in particular, had strong inverse associations with tree height. Nearly all measured traits varied significantly among genotypes, and several traits interacted with planting density, including aboveground biomass, root-shoot ratio, root fraction, branch angle, and crown depth. Semidwarfism promoted biomass allocation to roots over shoots and substantially increased rooting efficiency with most genes tested. The increased root proportion and increased leaf chlorophyll levels were associated with changes in leaf carbon isotope discrimination, indicating altered water use efficiency. Semidwarf trees had dramatically reduced growth when in direct competition with wild-type trees, supporting the hypothesis that semidwarfism genes could be effective tools to mitigate the spread of exotic, hybrid, and transgenic plants in wild and feral populations.

Chloroplast and nuclear microsatellite markers were used to study genetic diversity and genetic structure of Aegilops cylindrica Host collected in its native range and in adventive sites in the USA. Our analysis suggests that Ae. cylindrica, an allotetraploid, arose from multiple hybridizations between Ae. markgrafii (Greuter) Hammer. and Ae. tauschii Coss. presumably along the Fertile Crescent, where the geographic distributions of its diploid progenitors overlap. However, the center of genetic diversity of this species now encompasses a larger area including northern Iraq, eastern Turkey, and Transcaucasia. Although the majority of accessions of Ae. cylindrica (87%) had D-type plastomes derived from Ae. tauschii, accessions with C-type plastomes (13%), derived from Ae. markgrafii, were also observed. This corroborates a previous study suggesting the dimaternal origin of Ae. cylindrica. Model-based and genetic distance-based clustering using both chloroplast and nuclear markers indicated that Ae. tauschii ssp. tauschii contributed one of its D-type plastomes and its D genome to Ae. cylindrica. Analysis of genetic structure using nuclear markers suggested that Ae. cylindrica accessions could be grouped into three subpopulations (arbitrarily named N-K1, N-K2, and N-K3). Members of the N-K1 subpopulation were the most numerous in its native range and members of the N-K2 subpopulation were the most common in the USA. Our analysis also indicated that Ae. cylindrica accessions in the USA were derived from a few founder genotypes. The frequency of Ae. cylindrica accessions with the C-type plastome in the USA (approximately 24%) was substantially higher than in its native range of distribution (approximately 3%) and all C-type Ae. cylindrica in the USA except one belonged to subpopulation N-K2. The high frequency of the C-type plastome in the USA may reflect a favorable nucleo-cytoplasmic combination.

We tested the efficacy of an attenua- tion system developed to preclude the deleteri- ous effects of floral promoter::cytotoxin genes on vegetative growth of transgenic sterile plants. We tested the promoter (2.6 kb 5¢ region) of the poplar LEAFY gene PTLF driving barstar, combined on the same T-DNA with barstar dri- ven by either the CaMV 35S basal promoter +5 to -72 fragment (35SBP), 35SBP fused to the TMV omega element (35SBP omega), or the NOS promoter. The unattenuated pPTLF::barnase construct failed to give rise to any transgenic events, suggesting substantial non-reproductive expression from this promoter. The barstar- attenuated constructs enabled transformation, but the rate was reduced by nearly one-third. Four events (7% of attenuated events) had highly abnormal morphology, and were identified during the early phases of propagation; these events had significantly higher barnase:barstar expression ra- tios based on quantitative RT-PCR. A greenhouse study showed that phenotypically normal attenu- ated plants grew at the same rate as wild-type and barnase-lacking transgenic plants. A statistically significant positive linear association was found between relative growth rate (RGR) and bar- star:barnase ratio in the attenuated events, and graphical analysis suggested a threshold for barstar attenuation of barnase, above which additional levels of barstar did not provide further attenua- tion. Surprisingly, the appearance and growth rate of the nearly all of the attenuated events were substantially reduced after one or two growing seasons in the field, and the extent of growth reduction was associated with barstar:barnase expression ratio. These results demonstrate the importance of field testing during early phases of research to identify pleiotropic effects of transgenic sterility genes in trees.

Jointed goatgrass is an important weed of wheat in the United States and other parts of the world. Under field conditions, wheat and jointed goatgrass can hybridize and produce backcross derivatives, a situation that may allow gene flow between these two species. In order to gain a better understanding of the factors governing gene flow, a study to characterize patterns of mating between these two species was undertaken. Chloroplast and nuclear microsatellite markers were used to evaluate the parentage of 413 first-generation backcross (BC1) seeds obtained from 127 wheat–jointed goatgrass F1 hybrids, produced naturally under field conditions. Of the 127 hybrids evaluated, 109 (85.8%) had jointed goatgrass as the female parent, whereas the remaining 18 F1 plants (14.2%) had wheat as the female parent. Of the 413 BC1 plants analyzed, 358 (86.7%) had wheat and 24 (5.8%) had jointed goatgrass as the male backcross parent. The male parentage of 31 BC1 (7.5%) plants could not be determined. Under natur...

Aegilops cylindrica Host (2n = 4x = 28, genome CCDD) is an allotetraploid formed by hybridization between the diploid species Ae. tauschii Coss. (2n = 2x = 14, genome DD) and Ae. markgrafii (Greuter) Hammer (2n = 2x = 14, genome CC). Previous research has shown that Ae. tauschii contributed its cytoplasm to Ae. cylindrica. However, our analysis with chloroplast microsatellite markers showed that 1 of the 36 Ae. cylindrica accessions studied, TK 116 (PI 486249), had a plastome derived from Ae. markgrafii rather than Ae. tauschii. Thus, Ae. markgrafii has also contributed its cytoplasm to Ae. cylindrica. Our analysis of chloroplast and nuclear microsatellite markers also suggests that D-type plastome and the D genome in Ae. cylindrica were closely related to, and were probably derived from, the tauschii gene pool of Ae. tauschii. A determination of the likely source of the C genome and the C-type plastome in Ae. cylindrica was not possible.