Functional genomic effects of indels using Bayesian genome-phenome wide association studies in sorghum

High-throughput genomic and phenomic data have enhanced the ability to detect genotype-to-phenotype associations that can resolve broad pleiotropic effects of mutations on plant phenotypes. As the scale of genotyping and phenotyping has advanced, rigorous methodologies have been developed to accommodate larger datasets and maintain statistical precision. However, determining the functional effects of associated genes/loci is expensive and limited due to the complexity associated with cloning and subsequent characterization. Here, we utilized phenomic imputation of a multi-year, multi-environment dataset using PHENIX which imputes missing data using kinship and correlated traits, and we screened insertions and deletions (InDels) from the recently whole-genome sequenced Sorghum Association Panel for putative loss-of-function effects. Candidate loci from genome-wide association results were screened for potential loss of function using a Bayesian Genome-Phenome Wide Association Study (BGPWAS) model across both functionally characterized and uncharacterized loci. Our approach is designed to facilitate in silico validation of associations beyond traditional candidate gene and literature-search approaches and to facilitate the identification of putative variants for functional analysis and reduce the incidence of false-positive candidates in current functional validation methods. Using this Bayesian GPWAS model, we identified associations for previously characterized genes with known loss-of-function alleles, specific genes falling within known quantitative trait loci, and genes without any previous genome-wide associations while additionally detecting putative pleiotropic effects. In particular, we were able to identify the major tannin haplotypes at the Tan1 locus and effects of InDels on the protein folding. Depending on the haplotype present, heterodimer formation with Tan2 was significantly affected. We also identified major effect InDels in Dw2 and Ma1, where proteins were truncated due to frameshift mutations that resulted in early stop codons. These truncated proteins also lost most of their functional domains, suggesting that these indels likely result in loss of function. Here, we show that the Bayesian GPWAS model is able to identify loss-of-function alleles that can have significant effects upon protein structure and folding as well as multimer formation. Our approach to characterize loss-of-function mutations and their functional repercussions will facilitate precision genomics and breeding by identifying key targets for gene editing and trait integration

Clonal Selection of Sugar Cane for Texas and Louisiana from a Common Germplasm Pool

The sugar cane (a complex hybrid of Saccharum spp.) cultivar improvement program for the irrigated Lower Rio Grande Valley of Texas, initiated in 1961, has expanded greatly over the past 20 years. Initially, only 8 to 12 cultivars, selected from those previously released from commercial production in Louisiana or Florida, were screened annually for their production potential in the Lower Rio Grande Valley. The current introduction and screening program is more comprehensive utilizing 1) all clones advanced from the first to the second line trials at the U. S. Sugarcane Laboratory at Houma, Louisiana; 2) the advanced CP assignments from the U. S. Sugarcane Field Station, Canal Point, Florida; and 3) the L assignments from the Louisiana Agricultural Experiment Station, Baton Rouge, Louisiana. During the period 1981-83, 191 clones were assigned Texas ( TCP ) selection numbers. These clones were derived from crosses made at Canal Point but were selected in Texas from the early line trials. Only 10% of the lines selected in Texas were advanced to CP assignment status in Louisiana, the other 90% having been discarded. The difference in selections from a common germplasm pool was influenced by the response of clones to two contrasting environments and by the difference in selection criteria of the two programs

Genetic diversity of peanut (Arachis hypogaea L.) and its wild relatives based on the analysis of hypervariable regions of the genome

BACKGROUND: The genus Arachis is native to a region that includes Central Brazil and neighboring countries. Little is known about the genetic variability of the Brazilian cultivated peanut (Arachis hypogaea, genome AABB) germplasm collection at the DNA level. The understanding of the genetic diversity of cultivated and wild species of peanut (Arachis spp.) is essential to develop strategies of collection, conservation and use of the germplasm in variety development. The identity of the ancestor progenitor species of cultivated peanut has also been of great interest. Several species have been suggested as putative AA and BB genome donors to allotetraploid A. hypogaea. Microsatellite or SSR (Simple Sequence Repeat) markers are co-dominant, multiallelic, and highly polymorphic genetic markers, appropriate for genetic diversity studies. Microsatellite markers may also, to some extent, support phylogenetic inferences. Here we report the use of a set of microsatellite markers, including newly developed ones, for phylogenetic inferences and the analysis of genetic variation of accessions of A. hypogea and its wild relatives. RESULTS: A total of 67 new microsatellite markers (mainly TTG motif) were developed for Arachis. Only three of these markers, however, were polymorphic in cultivated peanut. These three new markers plus five other markers characterized previously were evaluated for number of alleles per locus and gene diversity using 60 accessions of A. hypogaea. Genetic relationships among these 60 accessions and a sample of 36 wild accessions representative of section Arachis were estimated using allelic variation observed in a selected set of 12 SSR markers. Results showed that the Brazilian peanut germplasm collection has considerable levels of genetic diversity detected by SSR markers. Similarity groups for A. hypogaea accessions were established, which is a useful criteria for selecting parental plants for crop improvement. Microsatellite marker transferability was up to 76% for species of the section Arachis, but only 45% for species from the other eight Arachis sections tested. A new marker (Ah-041) presented a 100% transferability and could be used to classify the peanut accessions in AA and non-AA genome carriers. CONCLUSION: The level of polymorphism observed among accessions of A. hypogaea analyzed with newly developed microsatellite markers was low, corroborating the accumulated data which show that cultivated peanut presents a relatively reduced variation at the DNA level. A selected panel of SSR markers allowed the classification of A. hypogaea accessions into two major groups. The identification of similarity groups will be useful for the selection of parental plants to be used in breeding programs. Marker transferability is relatively high between accessions of section Arachis. The possibility of using microsatellite markers developed for one species in genetic evaluation of other species greatly reduces the cost of the analysis, since the development of microsatellite markers is still expensive and time consuming. The SSR markers developed in this study could be very useful for genetic analysis of wild species of Arachis, including comparative genome mapping, population genetic structure and phylogenetic inferences among species

SSR Variation in Important U.S. Maize Inbred Lines

Historically important public inbred lines continue to play an important role in maize (Zea maysL.) improvement in many different breeding programs. Their continued use means they have undergone numerous seed increases in diverse programs since their original release. Our objective was to estimate the level of genetic diversity among and within inbred lines from different sources using SSR markers. We sampled six inbred lines (B73, CM105, Mo17, Oh43, W153R, and Wf9) obtained from 14 sources (breeding programs). The data were analyzed by analysis of molecular variance (AMOVA), genetic diversity statistics, and genetic distance (Dice\u27s coefficient). Of the total variation observed in gene frequency, 87.8% was found among inbred lines, 7.6% among sources within inbred lines, and 4.6% within sources. Genotypes of identically named inbred lines from eight different sources differed slightly on the basis of 44 SSR loci. The mean genetic similarity between sources of the same inbred was greater than 85%. It can be concluded that although more diversity exists among these six inbred lines than within them, a small but significant amount of variation exists among seed sources within inbreds. This variation may have arisen through differences in seed maintenance, since we found no evidence to suggest high mutation rates or extensive outcrossing. The small but statistically significant level of variation raises concerns in germplasm conservation, mapping studies, marker development, and long-term recombinant inbred line development, especially when high resolution is desired

Diversity Analysis of Elite Maize Inbred Lines Adapted to West and Central Africa Using SSR Markers

Seventeen elite maize inbred lines of West and Central Africa adaptation with tropical and temperate x tropical origin were investigated for diversity at 18 SSR loci in non-coding regions of the maize genome, alongside two temperate inbred lines (B73 and Mo17), perennial teosinte (Zea diploperennis) and gamagrass (Tripsacum dactyloides). A total of 174 alleles were detected with a range of 5 to 15 alleles per maker and an average of 9.7 alleles per locus. Polymorphic information content (PIC) ranged from 0.29 in umc1226 to 0.92 in bnlg2122 with an average of 0.75. Relationships between heterotic groups and groups based on SSR data were quite varied for the lines studied. Primarily, the SSR markers grouped the lines on the basis of their origin, with three instances of a pair of heterotic lines clustering together; one pair of temperate origin and the other two tropical vs temperate x tropical. Four inbred lines (CMR 19, CMR 20, CMR 21, and CMR 26), belonging to three heterotic groups were, however, differentiated by SSR data. The markers showed potential for use in managing inbred lines germplasm adapted to West and Central Africa, particularly for classifying inbred lines for which records of ancestry are not readily available and for exploiting the heterosis known for tropical vs. temperate x tropical crosses

Molecular Diversity, Structure and Domestication of Grasses

Over the last 10,000 years, crop domestication has been the single most important human cultural development. Grasses are prominent among these crops, and provide the vast majority of the world\u27s food. Similar traits have been selected during the domestication and breeding of these critically important grasses, and since they share a similar complement of genes, the same set of genes may have been selected. Even though the process of domestication occurred over the same 5000 to 10,000 year period, the domesticated grasses have major differences in genome structure, diversity, and life history. Molecular investigations of grass domestication have succeeded in identifying progenitor species and are beginning to catalog genetic resources. Additionally, research is now elucidating some of the basic processes by which crops have evolved over the last few millennia. In this review, we discuss our present knowledge of molecular diversity among the grass crops and relate that diversity to the genes involved in domestication and to yield gains. Understanding the connection between diversity and genome structure will be critical to future crop breeding

Sorghum Association Panel whole-genome sequencing establishes cornerstone resource for dissecting genomic diversity

Association mapping panels represent foundational resources for understanding the genetic basis of phenotypic diversity and serve to advance plant breeding by exploring genetic variation across diverse accessions. We report the whole-genome sequencing (WGS) of 400 sorghum (Sorghum bicolor (L.) Moench) accessions from the Sorghum Association Panel (SAP) at an average coverage of 38× (25–72×), enabling the development of a high-density genomic marker set of 43 983 694 variants including single-nucleotide polymorphisms (approximately 38 million), insertions/deletions (indels) (approximately 5 million), and copy number variants (CNVs) (approximately 170 000). We observe slightly more deletions among indels and a much higher prevalence of deletions among CNVs compared to insertions. This new marker set enabled the identification of several novel putative genomic associations for plant height and tannin content, which were not identified when using previous lower-density marker sets. WGS identified and scored variants in 5-kb bins where available genotyping-by-sequencing (GBS) data captured no variants, with half of all bins in the genome falling into this category. The predictive ability of genomic best unbiased linear predictor (GBLUP) models was increased by an average of 30% by using WGS markers rather than GBS markers. We identified 18 selection peaks across subpopulations that formed due to evolutionary divergence during domestication, and we found six Fst peaks resulting from comparisons between converted lines and breeding lines within the SAP that were distinct from the peaks associated with historic selection. This population has served and continues to serve as a significant public resource for sorghum research and demonstrates the value of improving upon existing genomic resources