Genetic Mapping by Sequencing More Precisely Detects Loci Responsible for Anaerobic Germination Tolerance in Rice

Ignacio, John Carlos I.; Zaidem, Maricris; Casal, Carlos; Dixit, Shalabh; Kretzschmar, Tobias; Samaniego, Jaime M.; Mendioro, Merlyn S.; Weigel, Detlef; Septiningsih, Endang M.

doi:10.3390/plants10040705

Cited by 8 publications

(6 citation statements)

References 49 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…To break this bottleneck, the gel-free and automated SNP marker system with high throughput, such as sequencing, was extensively developed. SNP markers have been developed and employed in rapeseed, maize, rice and bean [ 25 , 26 , 27 ]. Nevertheless, it is too expensive for most breeders to afford [ 18 , 28 ].…”

Section: Discussionmentioning

confidence: 99%

Development of the PARMS Marker of the Dominant Genic Male Sterility (DGMS) Line and Its Utilization in Rapeseed (Brassica napus L.) Breeding

Yuan

Wang

et al. 2022

Plants

View full text Add to dashboard Cite

The 8029AB line is a dominant genic male sterility (DGMS) two-type line in Brassica napus L., which can be used in a three-line approach for the seed production of rapeseed hybrids. Genetic analyses have demonstrated that the sterility of 8029A is controlled by a single dominant nuclear gene (BnMS5e) interacting with one recessive gene (BnMS5c). Six pairs of penta-primer amplification refractory mutation system (PARMS) markers were designed according to the sequence of BnMS5a, BnMS5c and BnMS5e. Two pairs of these PARMS markers were successfully identified and validated. The PARMS markers MS5-1Fc/MS5-1Ft/MS5-1R12 could distinguish BnMS5cfrom BnMS5a/BnMS5e, and the PARMS markers MS5-2Ft/MS5-2Fa/MS5-1R12 could genotype BnMS5aand BnMS5c/BnMS5e. The combination of these two pairs of PARMS markers could be used to identify the presence or absence of BnMS5a/BnMS5c/BnMS5e effectively. Consequently, marker-assisted selection can be carried out in the early generation to shorten the breeding period and improve the breeding efficiency.

show abstract

Section: Discussionmentioning

confidence: 99%

Development of the PARMS Marker of the Dominant Genic Male Sterility (DGMS) Line and Its Utilization in Rapeseed (Brassica napus L.) Breeding

Yuan

Wang

et al. 2022

Plants

View full text Add to dashboard Cite

show abstract

“…An alternative is to use the F 2:3 generation for more accurate phenotyping, although there is some QTL detection power lost due to segregation within families. Our work in rice for flooding-tolerant traits, for example, employed F 2:3 populations with good success [ 13 , 14 , 15 , 16 ]. Such populations can be generated in a short time; however, they have limited use due to constraints in the number of available seeds.…”

Section: Integrating Genetic Mapping and Genomics For Candidate Gene ...mentioning

confidence: 99%

Functional Allele Validation by Gene Editing to Leverage the Wealth of Genetic Resources for Crop Improvement

Thomson

Biswas

Tsakirpaloglou

et al. 2022

IJMS

Self Cite

View full text Add to dashboard Cite

Advances in molecular technologies over the past few decades, such as high-throughput DNA marker genotyping, have provided more powerful plant breeding approaches, including marker-assisted selection and genomic selection. At the same time, massive investments in plant genetics and genomics, led by whole genome sequencing, have led to greater knowledge of genes and genetic pathways across plant genomes. However, there remains a gap between approaches focused on forward genetics, which start with a phenotype to map a mutant locus or QTL with the goal of cloning the causal gene, and approaches using reverse genetics, which start with large-scale sequence data and work back to the gene function. The recent establishment of efficient CRISPR-Cas-based gene editing promises to bridge this gap and provide a rapid method to functionally validate genes and alleles identified through studies of natural variation. CRISPR-Cas techniques can be used to knock out single or multiple genes, precisely modify genes through base and prime editing, and replace alleles. Moreover, technologies such as protoplast isolation, in planta transformation, and the use of developmental regulatory genes promise to enable high-throughput gene editing to accelerate crop improvement.

show abstract

“…Initial quality control analyses of the whole-genome resequencing (WGRS) were carried out using the FastQC tool (Andrews, 2010) and then Trimmomatic (Bolger et al, 2014) was used to remove Illumina adapter sequences, filter reads shorter than 36 bp, and to trim the start and end of the sequences having quality lower than 5 (Ignacio et al, 2021). The trimmed sequences were then aligned to the Oryza sativa MSU release 7 reference genome 2 using the Burrows-Wheeler Alignment maximal exact matches sequence aligner (Li, 2013), and were subsequently sorted and assigned respective groups.…”

Section: Whole-genome Re-sequencing Analysis Between Parents and Hapl...mentioning

confidence: 99%

Genomic Regions and Floral Traits Contributing to Low Temperature Tolerance at Young Microspore Stage in a Rice (Oryza sativa L.) Recombinant Inbred Line Population of Sherpa/IRAT109

et al. 2022

View full text Add to dashboard Cite

Aerobic rice production (AP) consumes less water compared to flooded systems. Developing genotypes and identifying genomic regions associated with low temperature (LT) tolerance at the young microspore stage (YMS) is imperative for AP, particularly for temperate regions. Using a recombinant inbred line population derived from the Australian LT tolerant variety Sherpa, experiments were conducted to map and dissect quantitative trait loci (QTL) associated with spikelet sterility (SS) after exposure to LT and to investigate floral traits contributing to the development of lower SS. Significant genotypic variation for SS was observed in the population after exposure to LT at YMS. Three genomic regions associated with SS, qYMCT3, qYMCT4, and qYMCT8.1 were identified in chromosomes 3, 4, and 8 respectively, using multiple QTL models explaining 22.4% of the genotypic variation. Introgression of the favorable allele from qYMCT3 was estimated to reduce SS by up to 15.4%. A co-locating genomic region with qYMCT3, qDTHW3.1 was identified as the major QTL affecting days to heading and explained as much as 44.7% of the genotypic variation. Whole-genome sequence and bioinformatic analyses demonstrated OsMADS50 as the candidate gene for qYMCT3/qDTHW3.1 and to our knowledge, this was the first attempt in connecting the role of OsMADS50 in both LT and flowering in rice. Differential sets selected for extreme SS showed LT tolerant genotype group produced higher total pollen per spikelet resulting in a higher number of dehisced anthers and pollen on stigma and eventually, lower SS than THE sensitive group. The relationship between these key floral traits with SS was induced only after exposure to LT and was not observed in warm ideal temperature conditions. Identification of elite germplasm with favorable QTL allele and combinations, gene cloning, and pyramiding with additional high-value QTL for key traits should empower breeders to develop AP adapted genotypes for temperate growing regions, and ultimately produce climate-resilient rice.

show abstract

Genetic Mapping by Sequencing More Precisely Detects Loci Responsible for Anaerobic Germination Tolerance in Rice

Cited by 8 publications

References 49 publications

Development of the PARMS Marker of the Dominant Genic Male Sterility (DGMS) Line and Its Utilization in Rapeseed (Brassica napus L.) Breeding

Development of the PARMS Marker of the Dominant Genic Male Sterility (DGMS) Line and Its Utilization in Rapeseed (Brassica napus L.) Breeding

Functional Allele Validation by Gene Editing to Leverage the Wealth of Genetic Resources for Crop Improvement

Genomic Regions and Floral Traits Contributing to Low Temperature Tolerance at Young Microspore Stage in a Rice (Oryza sativa L.) Recombinant Inbred Line Population of Sherpa/IRAT109

Contact Info

Product

Resources

About