Discovery and Validation of Grain Shape Loci in U.S. Rice Germplasm Through Haplotype Characterization
Rice grain shape is a major determinant of rice market value and the end-use. We mapped quantitative trait loci (QTL) for grain shape traits in a bi-parental recombinant inbred line population (Trenasse/Jupiter) and discovered two major grain length QTLs—qGL3.1 and qGL7.1. Previously, a major grain...
| Main Authors: | , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Frontiers Media S.A.
2022-09-01
|
| Series: | Frontiers in Genetics |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/articles/10.3389/fgene.2022.923078/full |
| _version_ | 1811209708936101888 |
|---|---|
| author | Brijesh Angira Tommaso Cerioli Adam N. Famoso |
| author_facet | Brijesh Angira Tommaso Cerioli Adam N. Famoso |
| author_sort | Brijesh Angira |
| collection | DOAJ |
| description | Rice grain shape is a major determinant of rice market value and the end-use. We mapped quantitative trait loci (QTL) for grain shape traits in a bi-parental recombinant inbred line population (Trenasse/Jupiter) and discovered two major grain length QTLs—qGL3.1 and qGL7.1. Previously, a major grain shape gene GS3 was reported in the qGL3.1 region and grain length gene GL7 was reported to be encompassing qGL7.1 locus. The re-sequencing SNP data on the International Rice Research Institute (IRRI) 3K Rice Genome Project (RGP) panel were obtained from the IRRI SNP-Seek database for both genes and haplotype diversity was characterized for each gene in this diverse panel. United States rice germplasm was not well represented in the IRRI 3K RGP database. Therefore, a minimum SNP set was identified for each gene that could differentiate all the characterized haplotypes. These haplotypes in the 3K RGP panel were screened across 323 elite U.S. genotypes using the minimum SNP set. The screening of haplotypes and phenotype association confirmed the role of GS3 under qGL3.1. However, screening of the GL7 haplotypes in the U.S. germplasm panel showed that GL7 did not play a role in qGL7.1, and in addition, GL7.1 did not segregate in the Trenasse/Jupiter RIL population. This concluded that qGL7.1 is a novel QTL discovered on chr7 for grain shape in the Trenasse/Jupiter RIL population. A high-throughput KASP-based SNP marker for each locus (GS3 and qGL7.1) was identified and validated in elite U.S. rice germplasm to be used in an applied rice breeding program. |
| first_indexed | 2024-04-12T04:44:06Z |
| format | Article |
| id | doaj.art-d67c8f8947324f7cb8f0d17060e5bc8d |
| institution | Directory Open Access Journal |
| issn | 1664-8021 |
| language | English |
| last_indexed | 2024-04-12T04:44:06Z |
| publishDate | 2022-09-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Genetics |
| spelling | doaj.art-d67c8f8947324f7cb8f0d17060e5bc8d2022-12-22T03:47:33ZengFrontiers Media S.A.Frontiers in Genetics1664-80212022-09-011310.3389/fgene.2022.923078923078Discovery and Validation of Grain Shape Loci in U.S. Rice Germplasm Through Haplotype CharacterizationBrijesh Angira0Tommaso Cerioli1Adam N. Famoso2H. Rouse Caffey Rice Research Station, Louisiana State University Agricultural Center, Baton Rouge, LA, United StatesSchool of Plant, Environmental and Soil Science, Louisiana State University, Baton Rouge, LA, United StatesH. Rouse Caffey Rice Research Station, Louisiana State University Agricultural Center, Baton Rouge, LA, United StatesRice grain shape is a major determinant of rice market value and the end-use. We mapped quantitative trait loci (QTL) for grain shape traits in a bi-parental recombinant inbred line population (Trenasse/Jupiter) and discovered two major grain length QTLs—qGL3.1 and qGL7.1. Previously, a major grain shape gene GS3 was reported in the qGL3.1 region and grain length gene GL7 was reported to be encompassing qGL7.1 locus. The re-sequencing SNP data on the International Rice Research Institute (IRRI) 3K Rice Genome Project (RGP) panel were obtained from the IRRI SNP-Seek database for both genes and haplotype diversity was characterized for each gene in this diverse panel. United States rice germplasm was not well represented in the IRRI 3K RGP database. Therefore, a minimum SNP set was identified for each gene that could differentiate all the characterized haplotypes. These haplotypes in the 3K RGP panel were screened across 323 elite U.S. genotypes using the minimum SNP set. The screening of haplotypes and phenotype association confirmed the role of GS3 under qGL3.1. However, screening of the GL7 haplotypes in the U.S. germplasm panel showed that GL7 did not play a role in qGL7.1, and in addition, GL7.1 did not segregate in the Trenasse/Jupiter RIL population. This concluded that qGL7.1 is a novel QTL discovered on chr7 for grain shape in the Trenasse/Jupiter RIL population. A high-throughput KASP-based SNP marker for each locus (GS3 and qGL7.1) was identified and validated in elite U.S. rice germplasm to be used in an applied rice breeding program.https://www.frontiersin.org/articles/10.3389/fgene.2022.923078/fullricegrain shapegrain lengthQTLhaplotypeshigh-throughput KASP marker |
| spellingShingle | Brijesh Angira Tommaso Cerioli Adam N. Famoso Discovery and Validation of Grain Shape Loci in U.S. Rice Germplasm Through Haplotype Characterization Frontiers in Genetics rice grain shape grain length QTL haplotypes high-throughput KASP marker |
| title | Discovery and Validation of Grain Shape Loci in U.S. Rice Germplasm Through Haplotype Characterization |
| title_full | Discovery and Validation of Grain Shape Loci in U.S. Rice Germplasm Through Haplotype Characterization |
| title_fullStr | Discovery and Validation of Grain Shape Loci in U.S. Rice Germplasm Through Haplotype Characterization |
| title_full_unstemmed | Discovery and Validation of Grain Shape Loci in U.S. Rice Germplasm Through Haplotype Characterization |
| title_short | Discovery and Validation of Grain Shape Loci in U.S. Rice Germplasm Through Haplotype Characterization |
| title_sort | discovery and validation of grain shape loci in u s rice germplasm through haplotype characterization |
| topic | rice grain shape grain length QTL haplotypes high-throughput KASP marker |
| url | https://www.frontiersin.org/articles/10.3389/fgene.2022.923078/full |
| work_keys_str_mv | AT brijeshangira discoveryandvalidationofgrainshapelociinusricegermplasmthroughhaplotypecharacterization AT tommasocerioli discoveryandvalidationofgrainshapelociinusricegermplasmthroughhaplotypecharacterization AT adamnfamoso discoveryandvalidationofgrainshapelociinusricegermplasmthroughhaplotypecharacterization |