Article
Biotechnology & Applied Microbiology
Juanjuan Feng, Xuexian Zhang, Meng Zhang, Liping Guo, Tingxiang Qi, Huini Tang, Haiyong Zhu, Hailin Wang, Xiuqin Qiao, Chaozhu Xing, Jianyong Wu
Summary: This study successfully located the restore gene Rf(2) within a candidate interval of 1.48Mb on chromosome D05 by investigating fertility ratios, using BSA resequencing technology, high-throughput SNP genotyping, and InDel markers. The study also found that InDel markers co-segregated with Rf(2), enhancing the selection of the restorer line.
Article
Plant Sciences
Adem Bardak, Sadettin Celik, Oktay Erdogan, Remzi Ekinci, Ziya Dumlupinar
Summary: This study aimed to discover genetic markers associated with verticillium wilt in cotton. Through association mapping analysis, several SNP markers were identified to be associated with pathotypes and disease severity index, which could potentially be used in Marker Assisted Selection breeding for disease resistance in cotton.
Article
Genetics & Heredity
Suruchi Vij, Dharminder Pathak, Pankaj Rathore, Harish Kumar, P. S. Sekhon, Dharminder Bhatia, Parveen Chhuneja, Kuldeep Singh
Summary: This study reports for the first time the introgression and mapping of cotton leaf curl disease (CLCuD) resistance from a 'synthetic cotton polyploid' to upland cotton. It was found that CLCuD resistance exhibits dominance over susceptibility and two dominant genes were identified on chromosomes A01 and D07.
JOURNAL OF GENETICS
(2022)
Article
Biochemical Research Methods
Wei Quan, Bo Liu, Yadong Wang
Summary: This study introduces SALT, an SNP-aware alignment tool that efficiently maps reads to a reference genome incorporating an SNP database, resulting in improved accuracy. Experimental results demonstrate the superior performance of SALT in read alignment accuracy.
BMC BIOINFORMATICS
(2021)
Review
Biochemical Research Methods
Adrien Oliva, Raymond Tobler, Alan Cooper, Bastien Llamas, Yassine Souilmi
Summary: This study evaluated the performance of 30 mapping strategies implemented across four different read mapping software using simulated aDNA reads from three different human populations. The results show that specific parameterizations of NovoAlign, BWA-aln, and BWA-mem achieve high mapping precision with low levels of reference bias, especially after filtering out reads with low mapping qualities. The use of an IUPAC reference genome is necessary for achieving unbiased NovoAlign results in aDNA projects with reference population data.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Biochemical Research Methods
Alejandro Therese Navarro, Giorgio Tumino, Roeland E. Voorrips, Paul Arens, Marinus J. M. Smulders, Eric van de Weg, Chris Maliepaard
Summary: This study investigates the impact of genetic diversity on bi-allelic and multi-allelic models, and finds that using multi-allelic models can improve the detection power and accuracy of QTLs in populations with multiple functional QTL alleles.
BMC BIOINFORMATICS
(2022)
Review
Plant Sciences
Muhammad Yasir, Hafiza Hamrah Kanwal, Quaid Hussain, Muhammad Waheed Riaz, Muhammad Sajjad, Junkang Rong, Yurong Jiang
Summary: Over the past two decades, high-density SNP arrays and DNA sequencing technology have been widely used in crop research, particularly in cotton crops. Genome-wide association studies (GWAS) have provided an important tool for uncovering the relationship between crop phenotypes and underlying genetics, helping to advance crop breeding and improvement.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Plant Sciences
Ravi Prakash Shukla, Gopal Ji Tiwari, Babita Joshi, Kah Song-Beng, Sushma Tamta, N. Manikanda Boopathi, Satya Narayan Jena
Summary: A recombinant inbred line mapping population of intra-species upland cotton was generated, identifying 19 QTLs on nine chromosomes, with a notable drought tolerance QTL hotspot on chromosome 8.
PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS
(2021)
Article
Biochemical Research Methods
Jim Shaw, Yun William Yu
Summary: This paper introduces two new mathematical formulations for polyploid haplotype phasing, incorporated into the flopp method. Results show that flopp outperforms state-of-the-art algorithms in terms of speed and error reduction, demonstrating good performance in both simulated and real data.
JOURNAL OF COMPUTATIONAL BIOLOGY
(2022)
Article
Biochemical Research Methods
S. Karen Khatamifard, Zamshed Chowdhury, Nakul Pande, Meisam Razaviyayn, Chris Kim, Ulya R. Karpuzcu
Summary: DNA sequencing is an important process in genomic research. This paper introduces GeNVoM, a solution that improves the throughput and energy consumption of DNA sequencing by rethinking the algorithm and design of a non-volatile TCAM-based accelerator.
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
(2022)
Article
Biochemical Research Methods
Chirag Jain, Arang Rhie, Nancy F. Hansen, Sergey Koren, Adam M. Phillippy
Summary: Approximately 5-10% of the human genome is inaccessible due to the presence of repetitive sequences. Existing long-read mappers often yield incorrect alignments and variant calls within repetitive sequences. To address this issue, a new long-read mapping method called Winnowmap2 was developed, which is more tolerant of structural variation and more sensitive to paralog-specific variants within repeats.
Article
Biochemical Research Methods
Abhinav Dutta, David Pellow, Ron Shamir
Summary: We introduce parameterized syncmer schemes (PSS) as a generalization of syncmers and provide a theoretical analysis. By combining PSS with downsampling or minimizers, any desired compression and window guarantee can be achieved. The use of PSS in long-read mappers, such as minimap2 and Winnowmap2, shows improved mapping performance with fewer unmapped and incorrectly mapped reads across a wide range of datasets. The improvements are especially significant for low sequence identity and high compression.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Article
Biochemical Research Methods
Nastassia Gobet, Maxime Jan, Paul Franken, Ioannis Xenarios
Summary: Genetic variations have an impact on behavior and disease, but understanding how these variations contribute to complex traits is still a question. One common approach is to link genetic variants to intermediate phenotypes, such as the transcriptome, using RNA-sequencing. However, the variants between samples are often ignored in the initial analysis, which can lead to biased transcriptome estimation. In this study, the researchers assessed the impact of reference-based analysis on the transcriptome and expression quantitative trait locus (eQTLs) in a mouse genetic population. They found that using custom references improved downstream analysis compared to using the classical genome reference.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Article
Computer Science, Software Engineering
Sebastian Deorowicz, Adam Gudys
Summary: Identifying genetic variants is crucial in the era of precision medicine, and Whisper 2 is a short-read-mapping software that provides high-quality indel variant calling. It is among the fastest tools available.
Article
Agronomy
Guangzhi Mao, Hengling Wei, Pengyun Chen, Feng Xing, Hantao Wang
Summary: In this study, a high-density genetic map and genotyping method were used to identify QTLs for early-maturing traits, resulting in the discovery of stable QTLs and candidate genes. This research provides valuable information for fine mapping and breeding of early-maturing traits.