Genomics and molecular physiology for improvement of drought tolerance in wheat.

Abstract This chapter discusses the complexity of drought tolerance in wheat focusing the morphological, biochemical, physiological and molecular responses. The breeding approaches, such as traditional and genomics-assisted strategies, for drought tolerance in wheat are described. Future perspectives are also mentioned. Before wheat genome sequencing, it was very difficult to dissect drought tolerance genomic regions because of large genome size and repetitive sequences. But with the availability of sequencing approaches, a large number of genomic resources has become available which extend the scope of utilization of advanced genomics approaches such as GWAM and GS, MutMap+, etc. A new genome editing approach, the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPRassociated protein 9 (Cas9) system, can also be utilized for enhancement of drought tolerance in wheat. Therefore, integration of genomic approaches with precise phenotyping is the need of the hour for improving drought tolerance in wheat.

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Assessing genomic diversity and signatures of selection in Jiaxian Red cattle using whole-genome sequencing data

BMC Genomics ◽

10.1186/s12864-020-07340-0 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Xiaoting Xia ◽

Shunjin Zhang ◽

Huaju Zhang ◽

Zijing Zhang ◽

Ningbo Chen ◽

...

Keyword(s):

Population Structure ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Genomic Variation ◽

Genomic Diversity ◽

System Response ◽

Whole Genome ◽

Population Structure Analysis ◽

Native Cattle ◽

Genomic Regions

Abstract Background Native cattle breeds are an important source of genetic variation because they might carry alleles that enable them to adapt to local environment and tough feeding conditions. Jiaxian Red, a Chinese native cattle breed, is reported to have originated from crossbreeding between taurine and indicine cattle; their history as a draft and meat animal dates back at least 30 years. Using whole-genome sequencing (WGS) data of 30 animals from the core breeding farm, we investigated the genetic diversity, population structure and genomic regions under selection of Jiaxian Red cattle. Furthermore, we used 131 published genomes of world-wide cattle to characterize the genomic variation of Jiaxian Red cattle. Results The population structure analysis revealed that Jiaxian Red cattle harboured the ancestry with East Asian taurine (0.493), Chinese indicine (0.379), European taurine (0.095) and Indian indicine (0.033). Three methods (nucleotide diversity, linkage disequilibrium decay and runs of homozygosity) implied the relatively high genomic diversity in Jiaxian Red cattle. We used θπ, CLR, FST and XP-EHH methods to look for the candidate signatures of positive selection in Jiaxian Red cattle. A total number of 171 (θπ and CLR) and 17 (FST and XP-EHH) shared genes were identified using different detection strategies. Functional annotation analysis revealed that these genes are potentially responsible for growth and feed efficiency (CCSER1), meat quality traits (ROCK2, PPP1R12A, CYB5R4, EYA3, PHACTR1), fertility (RFX4, SRD5A2) and immune system response (SLAMF1, CD84 and SLAMF6). Conclusion We provide a comprehensive overview of sequence variations in Jiaxian Red cattle genomes. Selection signatures were detected in genomic regions that are possibly related to economically important traits in Jiaxian Red cattle. We observed a high level of genomic diversity and low inbreeding in Jiaxian Red cattle. These results provide a basis for further resource protection and breeding improvement of this breed.

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Chromosomal Map of the Model LegumeLotus japonicus

Genetics ◽

10.1093/genetics/161.4.1661 ◽

2002 ◽

Vol 161 (4) ◽

pp. 1661-1672 ◽

Cited By ~ 7

Author(s):

Andrea Pedrosa ◽

Niels Sandal ◽

Jens Stougaard ◽

Dieter Schweizer ◽

Andreas Bachmair

Keyword(s):

Repetitive Sequences ◽

Lotus Japonicus ◽

Chromosome Complement ◽

Linkage Groups ◽

Closely Related Species ◽

F1 Hybrid ◽

Bac Clones ◽

Genomic Regions ◽

Chromosomal Map

AbstractLotus japonicus is a model plant for the legume family. To facilitate map-based cloning approaches and genome analysis, we performed an extensive characterization of the chromosome complement of the species. A detailed karyotype of L. japonicus Gifu was built and plasmid and BAC clones, corresponding to genetically mapped markers (see the accompanying article by Sandal et al. 2002, this issue), were used for FISH to correlate genetic and chromosomal maps. Hybridization of DNA clones from 32 different genomic regions enabled the assignment of linkage groups to chromosomes, the comparison between genetic and physical distances throughout the genome, and the partial characterization of different repetitive sequences, including telomeric and centromeric repeats. Additional analysis of L. filicaulis and its F1 hybrid with L. japonicus demonstrated the occurrence of inversions between these closely related species, suggesting that these chromosome rearrangements are early events in speciation of this group.

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Wheat genome structure and function: genome sequence data and the International Wheat Genome Sequencing Consortium

Australian Journal of Agricultural Research ◽

10.1071/ar06155 ◽

2007 ◽

Vol 58 (6) ◽

pp. 470 ◽

Cited By ~ 11

Author(s):

P. Moolhuijzen ◽

D. S. Dunn ◽

M. Bellgard ◽

M. Carter ◽

J. Jia ◽

...

Keyword(s):

Genome Sequencing ◽

Physical Map ◽

Genome Structure ◽

Genetic Research ◽

Structure And Function ◽

Wheat Genome ◽

D Genome ◽

Genome Sequencing Consortium ◽

And Function ◽

Bac Contigs

Genome sequencing and the associated bioinformatics is now a widely accepted research tool for accelerating genetic research and the analysis of genome structure and function of wheat because it leverages similar work from other crops and plants. The International Wheat Genome Sequencing Consortium addresses the challenge of wheat genome structure and function and builds on the research efforts of Professor Bob McIntosh in the genetics of wheat. Currently, expressed sequence tags (ESTs; ~500 000 to date) are the largest sequence resource for wheat genome analyses. It is estimated that the gene coverage of the wheat EST collection is ~60%, close to that of Arabidopsis, indicating that ~40% of wheat genes are not represented in EST collections. The physical map of the D-genome donor species Aegilops tauschii is under construction (http://wheat.pw.usda.gov/PhysicalMapping). The technologies developed in this analysis of the D genome provide a good model for the approach to the entire wheat genome, namely compiling BAC contigs, assigning these BAC contigs to addresses in a high resolution genetic map, filling in gaps to obtain the entire physical length of a chromosome, and then large-scale sequencing.

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Patterns of genome size variation in snapping shrimp

Genome ◽

10.1139/gen-2015-0206 ◽

2016 ◽

Vol 59 (6) ◽

pp. 393-402 ◽

Cited By ~ 19

Author(s):

Nicholas W. Jeffery ◽

Kristin Hultgren ◽

Solomon Tin Chi Chak ◽

T. Ryan Gregory ◽

Dustin R. Rubenstein

Keyword(s):

Genome Size ◽

Phylogenetic Signal ◽

Size Variation ◽

Diverse Group ◽

Chromosome Size ◽

Genome Size Variation ◽

Large Genome ◽

Large Genome Size ◽

Single Genus ◽

Geographic Regions

Although crustaceans vary extensively in genome size, little is known about how genome size may affect the ecology and evolution of species in this diverse group, in part due to the lack of large genome size datasets. Here we investigate interspecific, intraspecific, and intracolony variation in genome size in 39 species of Synalpheus shrimps, representing one of the largest genome size datasets for a single genus within crustaceans. We find that genome size ranges approximately 4-fold across Synalpheus with little phylogenetic signal, and is not related to body size. In a subset of these species, genome size is related to chromosome size, but not to chromosome number, suggesting that despite large genomes, these species are not polyploid. Interestingly, there appears to be 35% intraspecific genome size variation in Synalpheus idios among geographic regions, and up to 30% variation in Synalpheus duffyi genome size within the same colony.

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Functional equivalence of genome sequencing analysis pipelines enables harmonized variant calling across human genetics projects

10.1101/269316 ◽

2018 ◽

Cited By ~ 1

Author(s):

Allison A. Regier ◽

Yossi Farjoun ◽

David Larson ◽

Olga Krasheninina ◽

Hyun Min Kang ◽

...

Keyword(s):

Data Processing ◽

Genome Sequencing ◽

Statistical Power ◽

Human Genetics ◽

Variant Calling ◽

Joint Analysis ◽

Sequencing Analysis ◽

Batch Effects ◽

Many Sources ◽

Genomic Regions

AbstractHundreds of thousands of human whole genome sequencing (WGS) datasets will be generated over the next few years to interrogate a broad range of traits, across diverse populations. These data are more valuable in aggregate: joint analysis of genomes from many sources increases sample size and statistical power for trait mapping, and will enable studies of genome biology, population genetics and genome function at unprecedented scale. A central challenge for joint analysis is that different WGS data processing and analysis pipelines cause substantial batch effects in combined datasets, necessitating computationally expensive reprocessing and harmonization prior to variant calling. This approach is no longer tenable given the scale of current studies and data volumes. Here, in a collaboration across multiple genome centers and NIH programs, we define WGS data processing standards that allow different groups to produce “functionally equivalent” (FE) results suitable for joint variant calling with minimal batch effects. Our approach promotes broad harmonization of upstream data processing steps, while allowing for diverse variant callers. Importantly, it allows each group to continue innovating on data processing pipelines, as long as results remain compatible. We present initial FE pipelines developed at five genome centers and show that they yield similar variant calling results – including single nucleotide (SNV), insertion/deletion (indel) and structural variation (SV) – and produce significantly less variability than sequencing replicates. Residual inter-pipeline variability is concentrated at low quality sites and repetitive genomic regions prone to stochastic effects. This work alleviates a key technical bottleneck for genome aggregation and helps lay the foundation for broad data sharing and community-wide “big-data” human genetics studies.

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Genetics of Germination and Seedling Traits under Drought Stress in a MAGIC Population of Maize

Plants ◽

10.3390/plants10091786 ◽

2021 ◽

Vol 10 (9) ◽

pp. 1786

Author(s):

Soumeya Rida ◽

Oula Maafi ◽

Ana López-Malvar ◽

Pedro Revilla ◽

Meriem Riache ◽

...

Keyword(s):

Drought Tolerance ◽

Genome Wide Association Study ◽

Genetic Regulation ◽

Breeding Programs ◽

Seedling Traits ◽

Genome Wide ◽

A Genome ◽

Positive Correlations ◽

Genomic Regions ◽

Magic Population

Drought is one of the most detrimental abiotic stresses hampering seed germination, development, and productivity. Maize is more sensitive to drought than other cereals, especially at seedling stage. Our objective was to study genetic regulation of drought tolerance at germination and during seedling growth in maize. We evaluated 420 RIL with their parents from a multi-parent advanced generation inter-cross (MAGIC) population with PEG-induced drought at germination and seedling establishment. A genome-wide association study (GWAS) was carried out to identify genomic regions associated with drought tolerance. GWAS identified 28 and 16 SNPs significantly associated with germination and seedling traits under stress and well-watered conditions, respectively. Among the SNPs detected, two SNPs had significant associations with several traits with high positive correlations, suggesting a pleiotropic genetic control. Other SNPs were located in regions that harbored major QTLs in previous studies, and co-located with QTLs for cold tolerance previously published for this MAGIC population. The genomic regions comprised several candidate genes related to stresses and plant development. These included numerous drought-responsive genes and transcription factors implicated in germination, seedling traits, and drought tolerance. The current analyses provide information and tools for subsequent studies and breeding programs for improving drought tolerance.

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Applications of genetic markers in cytogenetic manipulation of the wheat genomes

Genome ◽

10.1139/g89-025 ◽

1989 ◽

Vol 31 (1) ◽

pp. 137-142 ◽

Cited By ~ 17

Author(s):

M. D. Gale ◽

P. J. Sharp ◽

S. Chao ◽

C. N. Law

Keyword(s):

Restriction Fragment Length Polymorphism ◽

Restriction Fragment ◽

Length Polymorphism ◽

Fragment Length ◽

Fragment Length Polymorphism ◽

Genetic Maps ◽

Linkage Groups ◽

Large Genome ◽

Large Genome Size ◽

Restriction Fragment Length

A molecular map of wheat, Triticum aestivum, is being developed. Problems associated with the large genome size, the large number of linkage groups, polyploidy, and limited polymorphism at the DNA level are being overcome. In addition to the breeding applications expected from the map, various uses for restriction fragment length polymorphism markers as tools in cytogenetic manipulation of wheat chromosomes and those from related species are being found. These include identification of aneuploid genotypes, added precision in intervarietal chromosome manipulations, tests of chromosome stability, identification of alien chromosomes, and marker-aided introgression of genes of agronomic importance from related species.Key words: wheat, restriction fragment length polymorphism, genetic maps, aneuploidy, alien chromosomes.

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Fine-Mapping of Sorghum Stay-Green QTL on Chromosome10 Revealed Genes Associated with Delayed Senescence

Genes ◽

10.3390/genes11091026 ◽

2020 ◽

Vol 11 (9) ◽

pp. 1026 ◽

Cited By ~ 1

Author(s):

K. N. S. Usha Kiranmayee ◽

C. Tom Hash ◽

S. Sivasubramani ◽

P. Ramu ◽

Bhanu Prakash Amindala ◽

...

Keyword(s):

Drought Tolerance ◽

Fine Mapping ◽

Mapping Population ◽

Single Gene ◽

Genotyping By Sequencing ◽

Introgression Line ◽

Genomic Region ◽

Stay Green ◽

Delayed Senescence ◽

Genomic Regions

This study was conducted to dissect the genetic basis and to explore the candidate genes underlying one of the important genomic regions on an SBI-10 long arm (L), governing the complex stay-green trait contributing to post-flowering drought-tolerance in sorghum. A fine-mapping population was developed from an introgression line cross—RSG04008-6 (stay-green) × J2614-11 (moderately senescent). The fine-mapping population with 1894 F2 was genotyped with eight SSRs and a set of 152 recombinants was identified, advanced to the F4 generation, field evaluated with three replications over 2 seasons, and genotyped with the GBS approach. A high-resolution linkage map was developed for SBI-10L using 260 genotyping by sequencing—Single Nucleotide Polymorphism (GBS–SNPs). Using the best linear unpredicted means (BLUPs) of the percent green leaf area (%GL) traits and the GBS-based SNPs, we identified seven quantitative trait loci (QTL) clusters and single gene, mostly involved in drought-tolerance, for each QTL cluster, viz., AP2/ERF transcription factor family (Sobic.010G202700), NBS-LRR protein (Sobic.010G205600), ankyrin-repeat protein (Sobic.010G205800), senescence-associated protein (Sobic.010G270300), WD40 (Sobic.010G205900), CPK1 adapter protein (Sobic.010G264400), LEA2 protein (Sobic.010G259200) and an expressed protein (Sobic.010G201100). The target genomic region was thus delimited from 15 Mb to 8 genes co-localized with QTL clusters, and validated using quantitative real-time (qRT)–PCR.

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Polyploid polynuclear consecutive cell-cycle enables large genome-size in Haematococcus pluvialis

Algal Research ◽

10.1016/j.algal.2018.06.013 ◽

2018 ◽

Vol 33 ◽

pp. 456-461 ◽

Cited By ~ 2

Author(s):

Diana L. Reinecke ◽

Antonio Castillo-Flores ◽

Sammy Boussiba ◽

Aliza Zarka

Keyword(s):

Cell Cycle ◽

Genome Size ◽

Haematococcus Pluvialis ◽

Large Genome ◽

Large Genome Size

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Fine mapping of genomic regions associated with female fertility in Nellore beef cattle based on sequence variants from segregating sires

Journal of Animal Science and Biotechnology ◽

10.1186/s40104-019-0403-0 ◽

2019 ◽

Vol 10 (1) ◽

Author(s):

Gerson A. Oliveira Júnior ◽

Daniel J. A. Santos ◽

Aline S. M. Cesar ◽

Solomon A. Boison ◽

Ricardo V. Ventura ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Fine Mapping ◽

Reproductive Hormones ◽

Sequence Variants ◽

Whole Genome ◽

Biological Processes ◽

Snp Chip ◽

Mesh Terms ◽

Genomic Regions

Abstract Background Impaired fertility in cattle limits the efficiency of livestock production systems. Unraveling the genetic architecture of fertility traits would facilitate their improvement by selection. In this study, we characterized SNP chip haplotypes at QTL blocks then used whole-genome sequencing to fine map genomic regions associated with reproduction in a population of Nellore (Bos indicus) heifers. Methods The dataset comprised of 1337 heifers genotyped using a GeneSeek® Genomic Profiler panel (74677 SNPs), representing the daughters from 78 sires. After performing marker quality control, 64800 SNPs were retained. Haplotypes carried by each sire at six previously identified QTL on BTAs 5, 14 and 18 for heifer pregnancy and BTAs 8, 11 and 22 for antral follicle count were constructed using findhap software. The significance of the contrasts between the effects of every two paternally-inherited haplotype alleles were used to identify sires that were heterozygous at each QTL. Whole-genome sequencing data localized to the haplotypes from six sires and 20 other ancestors were used to identify sequence variants that were concordant with the haplotype contrasts. Enrichment analyses were applied to these variants using KEGG and MeSH libraries. Results A total of six (BTA 5), six (BTA 14) and five (BTA 18) sires were heterozygous for heifer pregnancy QTL whereas six (BTA 8), fourteen (BTA 11), and five (BTA 22) sires were heterozygous for number of antral follicles’ QTL. Due to inadequate representation of many haplotype alleles in the sequenced animals, fine mapping analysis could only be reliably performed for the QTL on BTA 5 and 14, which had 641 and 3733 concordant candidate sequence variants, respectively. The KEGG “Circadian rhythm” and “Neurotrophin signaling pathway” were significantly associated with the genes in the QTL on BTA 5 whereas 32 MeSH terms were associated with the QTL on BTA 14. Among the concordant sequence variants, 0.2% and 0.3% were classified as missense variants for BTAs 5 and 14, respectively, highlighting the genes MTERF2, RTMB, ENSBTAG00000037306 (miRNA), ENSBTAG00000040351, PRKDC, and RGS20. The potential causal mutations found in the present study were associated with biological processes such as oocyte maturation, embryo development, placenta development and response to reproductive hormones. Conclusions The identification of heterozygous sires by positionally phasing SNP chip data and contrasting haplotype effects for previously detected QTL can be used for fine mapping to identify potential causal mutations and candidate genes. Genomic variants on genes MTERF2, RTBC, miRNA ENSBTAG00000037306, ENSBTAG00000040351, PRKDC, and RGS20, which are known to have influence on reproductive biological processes, were detected.

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