Meta-QTL analysis in wheat: progress, challenges and opportunities
Theor Appl Genet. 2023 Nov 17;136(12):247. doi: 10.1007/s00122-023-04490-z.ABSTRACTWheat, an important cereal crop globally, faces major challenges due to increasing global population and changing climates. The production and productivity are challenged by several biotic and abiotic stresses. There is also a pressing demand to enhance grain yield and quality/nutrition to ensure global food and nutritional security. To address these multifaceted concerns, researchers have conducted numerous meta-QTL (MQTL) studies in wheat, resulting in the identification of candidate genes that govern these complex quantitative traits. MQT...
Source: TAG. Theoretical and Applied Genetics - November 17, 2023 Category: Genetics & Stem Cells Authors: Divya Sharma Anita Kumari Priya Sharma Anupma Singh Anshu Sharma Zahoor Ahmad Mir Uttam Kumar Sofora Jan M Parthiban Reyazul Rouf Mir Pradeep Bhati Anjan Kumar Pradhan Aakash Yadav Dwijesh Chandra Mishra Neeraj Budhlakoti Mahesh C Yadav Kiran B Gaikwad Am Source Type: research

Fine mapping and candidate gene analysis of qSB12 < sup > YSB < /sup > , a gene conferring major quantitative resistance to rice sheath blight
In this study, we identified a QTL on chromosome 12, in which the qSB12YSB resistant allele shows significant ShB resistance, by using 150 BC4 backcross inbred lines employing the resistant rice variety YSBR1 as the donor and the susceptible variety Lemont (LE) as the recurrent parent. We further fine-mapped qSB12YSB to a 289-kb region by generating 34 chromosomal segment substitution lines and identified a total of 18 annotated genes as the most likely candidates for qSB12YSB after analyzing resequencing and transcriptomic data. KEGG analysis suggested that qSB12YSB might activate secondary metabolites biosynthesis and RO...
Source: TAG. Theoretical and Applied Genetics - November 16, 2023 Category: Genetics & Stem Cells Authors: 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 Source Type: research

Genome-wide association study for temperature response and photo-thermal interaction of flowering time in soybean using a panel of cultivars with diverse maturity groups
Theor Appl Genet. 2023 Nov 14;136(12):245. doi: 10.1007/s00122-023-04496-7.ABSTRACTA total of 101 QTNs were found to be associated with soybean flowering time responses to photo-thermal conditions; three candidate genes with non-synonymous substitutions were identified: Glyma.08G302500 (GmHY5), Glyma.08G303900 (GmPIF4c), and Glyma.16G046700 (GmVRN1). The flowering transition is a crucial component of soybean (Glycine max L. Merr.) development. The transition process is regulated by photoperiod, temperature, and their interaction. To examine the genetic architecture associated with temperature- and photo-thermal-mediated re...
Source: TAG. Theoretical and Applied Genetics - November 14, 2023 Category: Genetics & Stem Cells Authors: Tingting Wu Huiwen Wen Xinyue Zhang Hongchang Jia Cailong Xu Wenwen Song Bingjun Jiang Shan Yuan Shi Sun Cunxiang Wu Tianfu Han Source Type: research

Genome-wide association study for temperature response and photo-thermal interaction of flowering time in soybean using a panel of cultivars with diverse maturity groups
Theor Appl Genet. 2023 Nov 14;136(12):245. doi: 10.1007/s00122-023-04496-7.ABSTRACTA total of 101 QTNs were found to be associated with soybean flowering time responses to photo-thermal conditions; three candidate genes with non-synonymous substitutions were identified: Glyma.08G302500 (GmHY5), Glyma.08G303900 (GmPIF4c), and Glyma.16G046700 (GmVRN1). The flowering transition is a crucial component of soybean (Glycine max L. Merr.) development. The transition process is regulated by photoperiod, temperature, and their interaction. To examine the genetic architecture associated with temperature- and photo-thermal-mediated re...
Source: TAG. Theoretical and Applied Genetics - November 14, 2023 Category: Genetics & Stem Cells Authors: Tingting Wu Huiwen Wen Xinyue Zhang Hongchang Jia Cailong Xu Wenwen Song Bingjun Jiang Shan Yuan Shi Sun Cunxiang Wu Tianfu Han Source Type: research

Genome-wide association study for temperature response and photo-thermal interaction of flowering time in soybean using a panel of cultivars with diverse maturity groups
Theor Appl Genet. 2023 Nov 14;136(12):245. doi: 10.1007/s00122-023-04496-7.ABSTRACTA total of 101 QTNs were found to be associated with soybean flowering time responses to photo-thermal conditions; three candidate genes with non-synonymous substitutions were identified: Glyma.08G302500 (GmHY5), Glyma.08G303900 (GmPIF4c), and Glyma.16G046700 (GmVRN1). The flowering transition is a crucial component of soybean (Glycine max L. Merr.) development. The transition process is regulated by photoperiod, temperature, and their interaction. To examine the genetic architecture associated with temperature- and photo-thermal-mediated re...
Source: TAG. Theoretical and Applied Genetics - November 14, 2023 Category: Genetics & Stem Cells Authors: Tingting Wu Huiwen Wen Xinyue Zhang Hongchang Jia Cailong Xu Wenwen Song Bingjun Jiang Shan Yuan Shi Sun Cunxiang Wu Tianfu Han Source Type: research

Genome wide association in Spanish bread wheat landraces identifies six key genomic regions that constitute potential targets for improving grain yield related traits
In this study, association mapping was conducted in a collection of 189 Spanish bread wheat landraces whose genomic diversity had been previously assessed. These genomic data were combined with characterization for yield-related traits, including grain size and shape, and phenological traits screened across five seasons. The association analysis revealed a total of 881 significant marker trait associations, involving 434 markers across the genome, that could be grouped in 366 QTLs based on linkage disequilibrium. After accounting for days to heading, we defined 33 high density QTL genomic regions associated to at least fou...
Source: TAG. Theoretical and Applied Genetics - November 13, 2023 Category: Genetics & Stem Cells Authors: Matilde L ópez-Fernández Juli án García-Abadillo Cristobal Uauy Magdalena Ruiz Patricia Giraldo Laura Pascual Source Type: research

A genomic analysis of the University of Nebraska Replicated Recurrent Selection program
The objectives of this study were to identify regions of the genome under selection after eight cycles of selection and evaluate the effect eight cycles of selection for inter-population full-sib performance had in expanding genome-wide and localized population structure. We address these questions with a large set of individuals sampled from the UNL-RpRS program with dense genotyping-by-sequence data. We found evidence of parallel selection signatures in the UNL-RpRS program, with a region on chromosome 7 being implicated in three of the four selection systems studied. Regions that displayed selection signatures across in...
Source: TAG. Theoretical and Applied Genetics - November 11, 2023 Category: Genetics & Stem Cells Authors: Collin M Lamkey Aaron J Lorenz Source Type: research

A genomic analysis of the University of Nebraska Replicated Recurrent Selection program
The objectives of this study were to identify regions of the genome under selection after eight cycles of selection and evaluate the effect eight cycles of selection for inter-population full-sib performance had in expanding genome-wide and localized population structure. We address these questions with a large set of individuals sampled from the UNL-RpRS program with dense genotyping-by-sequence data. We found evidence of parallel selection signatures in the UNL-RpRS program, with a region on chromosome 7 being implicated in three of the four selection systems studied. Regions that displayed selection signatures across in...
Source: TAG. Theoretical and Applied Genetics - November 11, 2023 Category: Genetics & Stem Cells Authors: Collin M Lamkey Aaron J Lorenz Source Type: research

A genomic analysis of the University of Nebraska Replicated Recurrent Selection program
The objectives of this study were to identify regions of the genome under selection after eight cycles of selection and evaluate the effect eight cycles of selection for inter-population full-sib performance had in expanding genome-wide and localized population structure. We address these questions with a large set of individuals sampled from the UNL-RpRS program with dense genotyping-by-sequence data. We found evidence of parallel selection signatures in the UNL-RpRS program, with a region on chromosome 7 being implicated in three of the four selection systems studied. Regions that displayed selection signatures across in...
Source: TAG. Theoretical and Applied Genetics - November 11, 2023 Category: Genetics & Stem Cells Authors: Collin M Lamkey Aaron J Lorenz Source Type: research

Simultaneous improvement of grain yield and grain protein concentration in durum wheat by using association tests and weighted GBLUP
Theor Appl Genet. 2023 Nov 10;136(12):242. doi: 10.1007/s00122-023-04487-8.ABSTRACTSimultaneous improvement for GY and GPC by using GWAS and GBLUP suggested a significant application in durum wheat breeding. Despite the importance of grain protein concentration (GPC) in determining wheat quality, its negative correlation with grain yield (GY) is still one of the major challenges for breeders. Here, a durum wheat panel of 200 genotypes was evaluated for GY, GPC, and their derived indices (GPD and GYD), under eight different agronomic conditions. The plant material was genotyped with the Illumina 25 k iSelect array, and a ge...
Source: TAG. Theoretical and Applied Genetics - November 10, 2023 Category: Genetics & Stem Cells Authors: Salvatore Esposito Paolo Vitale Francesca Taranto Sergio Saia Ivano Pecorella Nunzio D'Agostino Monica Rodriguez Vincenzo Natoli Pasquale De Vita Source Type: research

Simultaneous improvement of grain yield and grain protein concentration in durum wheat by using association tests and weighted GBLUP
Theor Appl Genet. 2023 Nov 10;136(12):242. doi: 10.1007/s00122-023-04487-8.ABSTRACTSimultaneous improvement for GY and GPC by using GWAS and GBLUP suggested a significant application in durum wheat breeding. Despite the importance of grain protein concentration (GPC) in determining wheat quality, its negative correlation with grain yield (GY) is still one of the major challenges for breeders. Here, a durum wheat panel of 200 genotypes was evaluated for GY, GPC, and their derived indices (GPD and GYD), under eight different agronomic conditions. The plant material was genotyped with the Illumina 25 k iSelect array, and a ge...
Source: TAG. Theoretical and Applied Genetics - November 10, 2023 Category: Genetics & Stem Cells Authors: Salvatore Esposito Paolo Vitale Francesca Taranto Sergio Saia Ivano Pecorella Nunzio D'Agostino Monica Rodriguez Vincenzo Natoli Pasquale De Vita Source Type: research

Improving yield-related traits by editing the promoter of the heading date gene Ehd1 in rice
In this study, we analyzed the cis-regulatory elements in the Ehd1 promoter region. We then used CRISPR/Cas9-mediated editing to modify the Ehd1 promoter at multiple target sites in ZJ8. We rapidly identified homozygous allelic mutations in the T2 generation via long-read sequencing. We obtained several Ehd1 promoter mutants with different degrees of lower Ehd1 expression, delayed heading date, and improved yield-related traits. We developed an efficient promoter editing method to create different weak Ehd1 alleles for breeding selection. Using this method, a series of heading date materials from elite varieties can be cre...
Source: TAG. Theoretical and Applied Genetics - November 6, 2023 Category: Genetics & Stem Cells Authors: Shengting Li Yanqiu Luo Guangliang Wei Wubei Zong Wanyong Zeng Dongdong Xiao Han Zhang Yingang Song Yu Hao Kangli Sun Chen Lei Xiaotong Guo Bingqun Xu Weitao Li Zeqiang Wu Yaoguang Liu Xianrong Xie Jingxin Guo Source Type: research

Dissection and validation of a promising QTL controlling spikelet number on 5B in bread wheat
In this study, a high-density genetic map for a recombinant inbred lines (RILs) population derived from Zhengnong 17 (ZN17) and Yangbaimai (YBM) was constructed using 95,444 single-nucleotide polymorphism (SNP) markers from the Wheat660K SNP array. Our study identified a total of five environmentally stable QTLs for SNS and DTH, one of which was named QSns.ucas-5B, with a physical interval of approximately 545.4-552.1 Mb on the 5BL chromosome arm. Importantly, the elite haplotype within QSns.ucas-5B showed a consistent and positive effect on SNS, grain number and weight per spike, without extending the days to heading. The...
Source: TAG. Theoretical and Applied Genetics - November 6, 2023 Category: Genetics & Stem Cells Authors: Yaoqi Si Shuiquan Tian Jianqing Niu Zhongqing Yu Shengwei Ma Qiao Lu Huilan Wu Hong-Qing Ling Shusong Zheng Source Type: research

Seed color in lettuce is determined by the LsTT2, LsCHS, and Ls2OGD genes from the flavonoid biosynthesis pathway
This study provides new insights into the regulation of flavonoid biosynthesis in plants.PMID:37930450 | DOI:10.1007/s00122-023-04491-y (Source: TAG. Theoretical and Applied Genetics)
Source: TAG. Theoretical and Applied Genetics - November 6, 2023 Category: Genetics & Stem Cells Authors: Xiaoyan Zhang Xiaoli Liang Shuping He Hao Tian Wenye Liu Yue Jia Lei Zhang Weiyi Zhang Hanhui Kuang Jiongjiong Chen Source Type: research

Improving yield-related traits by editing the promoter of the heading date gene Ehd1 in rice
In this study, we analyzed the cis-regulatory elements in the Ehd1 promoter region. We then used CRISPR/Cas9-mediated editing to modify the Ehd1 promoter at multiple target sites in ZJ8. We rapidly identified homozygous allelic mutations in the T2 generation via long-read sequencing. We obtained several Ehd1 promoter mutants with different degrees of lower Ehd1 expression, delayed heading date, and improved yield-related traits. We developed an efficient promoter editing method to create different weak Ehd1 alleles for breeding selection. Using this method, a series of heading date materials from elite varieties can be cre...
Source: TAG. Theoretical and Applied Genetics - November 6, 2023 Category: Genetics & Stem Cells Authors: Shengting Li Yanqiu Luo Guangliang Wei Wubei Zong Wanyong Zeng Dongdong Xiao Han Zhang Yingang Song Yu Hao Kangli Sun Chen Lei Xiaotong Guo Bingqun Xu Weitao Li Zeqiang Wu Yaoguang Liu Xianrong Xie Jingxin Guo Source Type: research