Article
Biochemical Research Methods
Jing Chen, Lindsey J. Leach, Zewei Luo
Summary: Mapping quantitative trait loci (QTL) in autotetraploid species is a timely and challenging task. Two papers by Wu and his colleagues proposed statistical methods for QTL mapping in these species, but have been criticized for fundamental conceptual errors from statistical and genetic perspectives.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Biochemistry & Molecular Biology
Jae-Ryoung Park, Yoon-Hee Jang, Eun-Gyeong Kim, Sang-Sun Hur, Kyung-Min Kim, Deyong Ren
Summary: In this study, QTLs and candidate genes related to rice plant height regulation were identified, which can provide information and foundation for marker-assisted selection and breeding.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Plant Sciences
Gurpreet Kaur, Mamta Pathak, Deepak Singla, Gautam Chhabra, Parveen Chhuneja, Navraj Kaur Sarao
Summary: This study used genotyping-by-sequencing to genotype bitter gourd and detected genetic loci controlling earliness, fruit, and seed traits. A total of 50 QTLs were detected, explaining 5.09% to 29.82% of the phenotypic variance.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Agronomy
Magdalena Gawlowska, Michal Knopkiewicz, Wojciech swiecicki, Lech Boros, Anna Wawer
Summary: Studying the relationship between stem mechanical parameters and lodging in pea, researchers identified 9 QTL associated with lodging resistance in different pea cultivars. These results lay a foundation for further research aiming to improve lodging resistance in pea.
Article
Plant Sciences
Ana Pina, Patricia Irisarri, Pilar Errea, Tetyana Zhebentyayeva
Summary: This study investigated graft incompatibility using next-generation sequencing technology and successfully constructed parental linkage maps between Prunus rootstocks and apricot cultivars. By analyzing SNP markers and phenotypic data, QTLs affecting graft compatibility were identified.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Agronomy
Yu Wang, Quanyi Sun, Jianhua Zhao, Taixuan Liu, Haibo Du, Wenfeng Shan, Keting Wu, Xiang Xue, Chao Yang, Jun Liu, Zongxiang Chen, Keming Hu, Zhiming Feng, Shimin Zuo
Summary: This study identified a QTL for sheath blight resistance in rice and further fine-mapped it to a specific region. Functional analysis suggested that this QTL might enhance resistance to sheath blight through the activation of secondary metabolites biosynthesis and ROS scavenging system. Field trials demonstrated that this QTL conferred stable resistance and significantly reduced yield losses. These findings will contribute to the isolation of the QTL and its utilization in rice breeding programs against sheath blight.
THEORETICAL AND APPLIED GENETICS
(2023)
Article
Agriculture, Dairy & Animal Science
Chiara Rizzi, Filippo Cendron, Mauro Penasa, Martino Cassandro
Summary: This study compared yield performance and egg physical characteristics of eight autochthonous chicken breeds in the Veneto region of Italy. The results showed differences in yield and egg quality among the breeds, allowing consumers to choose eggs of different qualities based on their cooking purposes.
Article
Horticulture
Fengming Li, Zhiyuan Liu, Haixu Chen, Jian Wu, Xu Cai, Hui Wang, Xiaowu Wang, Jianli Liang
Summary: In this study, a high-density bin map was constructed to locate 60 significant QTLs controlling 11 leaf-related traits. Candidate genes responsible for these complex traits were identified. The cost-effective bin-mapping approach can accelerate the improvement of Brassica rapa vegetable breeding by rapidly identifying QTLs and candidate genes.
Correction
Agronomy
Tianheng Ren, Tao Fan, Shulin Chen, Chunsheng Li, Yongyan Chen, Xia Ou, Qing Jiang, Zhenglong Ren, Feiquan Tan, Peigao Luo, Chen Chen, Zhi Li
Summary: The stable QTL associated with KWPS, SN, KDR, KW, KL, TKW and PH have been identified and located on chromosomes using a 371 RIL population derived from a cross between CN18 and T1208. Clear QTL clusters were observed on the chromosomes.
THEORETICAL AND APPLIED GENETICS
(2021)
Article
Plant Sciences
Nadia Valentini, Ezio Portis, Roberto Botta, Alberto Acquadro, Vera Pavese, Emile Cavalet Giorsa, Daniela Torello Marinoni
Summary: This study aimed to identify quantitative trait loci (QTLs) related to hazelnut phenotypic traits, including timing of male and female flowering, dichogamy, and time required for nut maturity. Using a population of F-1 progeny bred from the cross Tonda Gentile delle Langhe x Merveille de Bollwiller, a total of 42 QTL-harboring regions were identified, with 21 classified as major.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Plant Sciences
Na Zhao, Dong Xue, Yamei Miao, Yongqiang Wang, Enqiang Zhou, Yao Zhou, Mengnan Yao, Chunyan Gu, Kaihua Wang, Bo Li, Libin Wei, Xuejun Wang
Summary: In this study, an ultra-dense genetic map of faba bean was constructed using next-generation sequencing genotyping platform. A total of 65 QTLs for seed-related traits and 333 candidate genes were identified. These findings have significant implications for marker-assisted breeding and improvement of the faba bean genome.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Agronomy
Modester Kachapila, Yuki Horiuchi, Hidetaka Nagasawa, Noe Michihata, Toru Yoshida, Yuta Kato, Paul C. Bethke, Kiyoaki Kato, Masahiko Mori
Summary: By studying the progeny of a cross between two bean cultivars, four genetic loci that affect epicotyl length were found, and the chromosomal location of one of these loci was narrowed down using molecular markers, which can be used for selecting bean cultivars with longer epicotyls that are suitable for mechanical weeding and harvesting.
Article
Plant Sciences
Yuefeng Ruan, Bianyun Yu, Ron E. Knox, Wentao Zhang, Asheesh K. Singh, Richard Cuthbert, Pierre Fobert, Ron DePauw, Samia Berraies, Andrew Sharpe, Bin Xiao Fu, Jatinder Sangha
Summary: In the genetic study of durum wheat in Canada, QTL mapping was conducted to identify loci associated with grain protein concentration (GPC). Several major and minor QTL were discovered on different chromosomes, with some being consistently detected across multiple years and showing potential for improving both GPC and grain yield. The results of traditional and conditional mapping provide valuable insights for the development of high GPC and high yielding durum cultivars.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Plant Sciences
Jing Wu, Lili Mao, Jincai Tao, Xiuxiu Wang, Haijun Zhang, Ming Xin, Yongqi Shang, Yanan Zhang, Guihua Zhang, Zhongting Zhao, Yiming Wang, Mingshuo Cui, Liming Wei, Xianliang Song, Xuezhen Sun
Summary: This study used a genetic map and phenotype data to analyze the QTL of plant height in cotton, identifying several stable and unconditional QTL and revealing the dynamic expression characteristics of genes related to plant height development. Additionally, through functional annotation and transcriptome analysis, candidate genes potentially involved in plant height development were predicted.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Agronomy
An Yan, Songrui Ning, Hongwei Geng, Tao Guo, Shuting Xiao
Summary: The application of UAV remote sensing technology is important for monitoring plant height in wheat varieties. A low-altitude remote sensing platform was built using a high-resolution digital camera mounted on a UAV to obtain images of a wheat population. Plant height extraction models were constructed using actual plant height measurements and a DSM. QTL analysis was performed using UAV plant height data and a SNP chip to detect loci related to plant height.
Article
Agriculture, Dairy & Animal Science
B. H. Essa, S. Suzuki, A. J. Nagano, S. Z. Elkholya, A. Ishikawa
Summary: Genome-wide QTL analysis in an F-2 population derived from Nagoya chickens and White Plymouth Rock revealed three key loci influencing early growth. The most significant QTL on GGA4 showed effects on multiple traits, suggesting its potential for genetic improvement of growth performance in the Nagoya breed.
Article
Agriculture, Dairy & Animal Science
Tatsuhiko Goto, Saki Shimamoto, Akira Ohtsuka, Daichi Ijiri
Summary: By investigating the impact of different chicken breeds and feeds on the amino acid contents and bitterness sensor traits of eggs, it was found that breeds and feeds significantly influenced bitterness in the albumen and yolk, with limited effects on amino acid traits. The results suggest that selecting the right combination of breed and feed can result in customized eggs with enriched amino acids and enhanced taste.
ANIMAL SCIENCE JOURNAL
(2021)
Article
Behavioral Sciences
Yuki Matsumoto, Hiromichi Nagayama, Hirofumi Nakaoka, Atsushi Toyoda, Tatsuhiko Goto, Tsuyoshi Koide
Summary: Through selective breeding, significant changes in active tameness behaviors were observed in nine tameness-related traits in mice, including contacting and heading. At the gene expression level, differential expression of 136 genes was found between the selection and control groups, with pathway analysis identifying networks associated with these genes. These results suggest that changes in gene expression networks may drive the emergence of active tameness in selected populations.
GENES BRAIN AND BEHAVIOR
(2021)
Article
Genetics & Heredity
Mohammad Ibrahim Haqani, Shigeru Nomura, Michiharu Nakano, Tatsuhiko Goto, Atsushi J. Nagano, Atsushi Takenouchi, Yoshiaki Nakamura, Akira Ishikawa, Masaoki Tsudzuki
Summary: This research identified QTL associated with egg-related traits in Japanese quail by constructing a genetic linkage map using RAD-seq. Nine QTL affecting 10 egg traits were identified, including egg weight, egg shell strength, yolk weight, albumen weight, etc. This study demonstrates the effectiveness of RAD-seq for QTL analysis and marker-assisted selection in poultry industry, particularly in Japanese quail.
Article
Biochemistry & Molecular Biology
Mohammad Ibrahim Haqani, Shigeru Nomura, Michiharu Nakano, Tatsuhiko Goto, Atsushi J. Nagano, Atsushi Takenouchi, Yoshiaki Nakamura, Akira Ishikawa, Masaoki Tsudzuki
Summary: This study constructed a genetic linkage map using SNP markers to identify QTLs for growth-related traits in Japanese quail. Analysis revealed four main-effect QTLs associated with body weight and asymptotic weight of the Richards model. These results suggest that QTL studies and the RAD-seq method could be beneficial for future breeding programs in the poultry industry.
MOLECULAR GENETICS AND GENOMICS
(2021)
Article
Agriculture, Dairy & Animal Science
Ryoko Ono, Haruka Miyachi, Harui Usui, Rina Oguchi, Kenji Nishimura, Kanna Takahashi, Yuri Yamagishi, Nonoka Kawamura, Remi Matsushita, Tatsuhiko Goto
Summary: This study investigated the changes in various traits in three genetically distinct Japanese indigenous chicken breeds during different growth stages. The results showed significant differences in traits among breeds and between sexes during growth stages. Additionally, the shape and length of the tail feathers, tail number, body weight, and shank length exhibited age-dependent changes.
JOURNAL OF POULTRY SCIENCE
(2022)
Article
Agriculture, Dairy & Animal Science
Tatsuhiko Goto, Kosei Ohya, Masahiro Takaya
Summary: This study investigates the effects of genetic background on egg traits in chickens by using different chicken genotypes. The results show that genetic background not only affects the size and weight of eggs but also the amino acid contents and balance of yolk and albumen.
Article
Genetics & Heredity
Takaya Nakano, Momoko Takenaka, Makoto Sugiyama, Akira Ishikawa
Summary: This study aimed to map major QTLs for a novel pigmentation phenotype in mice and analyze the expression levels of four important melanogenesis genes. They discovered a significant QTL for eye pigmentation on chromosome 13, which may control complex melanin biosynthesis.
Article
Multidisciplinary Sciences
Naru Babaya, Michiko Itoi-Babaya, Hironori Ueda, Misato Kobayashi, Shinsuke Noso, Yoshihisa Hiromine, Akira Ishikawa, Tomomi Fujisawa, Hiroshi Ikegami
Summary: We identified four new quantitative trait loci (QTLs) for hyperglycemia in the Nagoya-Shibata-Yasuda (NSY) mouse model, specifically on Chromosome 1, 4, 10, and 13. These QTLs were associated with hyperglycemia in young mice and had attenuated effects in older mice. Our findings highlight the importance of longitudinal phenotypes in genetic analysis of polygenic traits and have implications for understanding the genetic basis and pathogenesis of type 2 diabetes in humans.
SCIENTIFIC REPORTS
(2023)
Article
Genetics & Heredity
Takayuki Ochiai, Marina Sakaguchi, Shin-Ichi Kawakami, Akira Ishikawa
Summary: An integrated approach of transcriptome, haplotype frequency, and association analyses was used to identify candidate genes for the QTL affecting innate fear behavioral traits in chickens. The initial QTL interval on chromosome 4 contained 333 genes, but through further analysis, the number of candidate genes was reduced to 11, with NPY5R and LOC101749214 identified as strong candidates for innate fear behavior.
G3-GENES GENOMES GENETICS
(2023)
Article
Agriculture, Dairy & Animal Science
M. Terashima, V. V. Velasco, N. Goto, M. Tsudzuki, A. Ishikawa
Summary: Comprehensive knowledge of innate fear in chickens has implications for understanding the adaptation and behavioural changes in native Japanese chickens. Through TI and OF tests, it was found that Oh-Shamo was the least sensitive breed to fear.
BRITISH POULTRY SCIENCE
(2023)
Article
Agriculture, Dairy & Animal Science
Nonoka Kawamura, Masahiro Takaya, Hideaki Hayashi, Tatsuhiko Goto
Summary: Many countries have transitioned to animal welfare-friendly housing systems for egg layers, but there is still no consensus on whether these systems affect egg quality traits. This study investigated the effects of two housing systems, conventional cages and floor rearing, on egg traits and amino acid contents in albumen and yolk. The results showed significant effects of the housing systems on body weight gain, eggshell weight, yolk weight, eggshell thickness, eggshell lightness, and several albumen amino acids. Notably, even after switching housing systems, eggshell lightness remained significantly affected. These findings suggest that different housing systems can impact egg traits, including albumen amino acid contents.
Article
Agriculture, Dairy & Animal Science
Vanessa Viterbo Velasco, Takayuki Ochiai, Masaoki Tsudzuki, Naoki Goto, Akira Ishikawa
Summary: Understanding the genetic mechanisms underlying innate fear behavior has important implications for the poultry industry. This study identified significant QTL associated with innate fear responses in chickens, providing valuable insights for improving management and breeding strategies.
Article
Biology
Tatsuhiko Goto, Satoshi Konno, Miwa Konno
Summary: The purpose of this study was to conduct a field study and create wild-derived quail strains using the breeding stocks in Tokachi, Hokkaido, Japan. Field observations show that adult males have intermittent reproductive opportunities from May to August. By utilizing natural mating between captured wild males and domestic females, the W50 and W75 strains, with 50% and 75% genetic contributions from the wild stocks, were established for future conservation and experimental use.
Article
Agriculture, Dairy & Animal Science
Mohammad Haqani, Kensuke Kawamura, Atsushi Takenouchi, Mohammad H. Kabir, Yoshiaki Nakamura, Akira Ishikawa, Masaoki Tsudzuki
Summary: This study compared the growth patterns of large- and normal-sized Japanese quail strains and their F-1 progeny, finding that the Richards and Gompertz models best described their growth characteristics. Additionally, it was observed that the growth pattern of the F-1 birds may have been inherited from the male parental strain.
JOURNAL OF POULTRY SCIENCE
(2021)
