Dissection of the E8 locus in two early maturing Canadian soybean populations
Soybean [Glycine max (L.) Merr.] is a short-day crop for which breeders want to expand the cultivation range to more northern agro-environments by introgressing alleles involved in early reproductive traits. To do so, we investigated quantitative trait loci (QTL) and expression quantitative trait lo...
| Main Authors: | , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Frontiers Media S.A.
2024-02-01
|
| Series: | Frontiers in Plant Science |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/articles/10.3389/fpls.2024.1329065/full |
| _version_ | 1797321065129574400 |
|---|---|
| author | Jérôme Gélinas Bélanger Jérôme Gélinas Bélanger Tanya Rose Copley Valerio Hoyos-Villegas Louise O’Donoughue |
| author_facet | Jérôme Gélinas Bélanger Jérôme Gélinas Bélanger Tanya Rose Copley Valerio Hoyos-Villegas Louise O’Donoughue |
| author_sort | Jérôme Gélinas Bélanger |
| collection | DOAJ |
| description | Soybean [Glycine max (L.) Merr.] is a short-day crop for which breeders want to expand the cultivation range to more northern agro-environments by introgressing alleles involved in early reproductive traits. To do so, we investigated quantitative trait loci (QTL) and expression quantitative trait loci (eQTL) regions comprised within the E8 locus, a large undeciphered region (~7.0 Mbp to 44.5 Mbp) associated with early maturity located on chromosome GM04. We used a combination of two mapping algorithms, (i) inclusive composite interval mapping (ICIM) and (ii) genome-wide composite interval mapping (GCIM), to identify major and minor regions in two soybean populations (QS15524F2:F3 and QS15544RIL) having fixed E1, E2, E3, and E4 alleles. Using this approach, we identified three main QTL regions with high logarithm of the odds (LODs), phenotypic variation explained (PVE), and additive effects for maturity and pod-filling within the E8 region: GM04:16,974,874-17,152,230 (E8-r1); GM04:35,168,111-37,664,017 (E8-r2); and GM04:41,808,599-42,376,237 (E8-r3). Using a five-step variant analysis pipeline, we identified Protein far-red elongated hypocotyl 3 (Glyma.04G124300; E8-r1), E1-like-a (Glyma.04G156400; E8-r2), Light-harvesting chlorophyll-protein complex I subunit A4 (Glyma.04G167900; E8-r3), and Cycling dof factor 3 (Glyma.04G168300; E8-r3) as the most promising candidate genes for these regions. A combinatorial eQTL mapping approach identified significant regulatory interactions for 13 expression traits (e-traits), including Glyma.04G050200 (Early flowering 3/E6 locus), with the E8-r3 region. Four other important QTL regions close to or encompassing major flowering genes were also detected on chromosomes GM07, GM08, and GM16. In GM07:5,256,305-5,404,971, a missense polymorphism was detected in the candidate gene Glyma.07G058200 (Protein suppressor of PHYA-105). These findings demonstrate that the locus known as E8 is regulated by at least three distinct genomic regions, all of which comprise major flowering genes. |
| first_indexed | 2024-03-08T04:52:09Z |
| format | Article |
| id | doaj.art-f46130642fe748dba56853042cea66ba |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-03-08T04:52:09Z |
| publishDate | 2024-02-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj.art-f46130642fe748dba56853042cea66ba2024-02-08T04:32:11ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2024-02-011510.3389/fpls.2024.13290651329065Dissection of the E8 locus in two early maturing Canadian soybean populationsJérôme Gélinas Bélanger0Jérôme Gélinas Bélanger1Tanya Rose Copley2Valerio Hoyos-Villegas3Louise O’Donoughue4Centre de recherche sur les grains (CÉROM) Inc., St-Mathieu-de-Beloeil, QC, CanadaDepartment of Plant Science, McGill University, Montréal, QC, CanadaCentre de recherche sur les grains (CÉROM) Inc., St-Mathieu-de-Beloeil, QC, CanadaDepartment of Plant Science, McGill University, Montréal, QC, CanadaCentre de recherche sur les grains (CÉROM) Inc., St-Mathieu-de-Beloeil, QC, CanadaSoybean [Glycine max (L.) Merr.] is a short-day crop for which breeders want to expand the cultivation range to more northern agro-environments by introgressing alleles involved in early reproductive traits. To do so, we investigated quantitative trait loci (QTL) and expression quantitative trait loci (eQTL) regions comprised within the E8 locus, a large undeciphered region (~7.0 Mbp to 44.5 Mbp) associated with early maturity located on chromosome GM04. We used a combination of two mapping algorithms, (i) inclusive composite interval mapping (ICIM) and (ii) genome-wide composite interval mapping (GCIM), to identify major and minor regions in two soybean populations (QS15524F2:F3 and QS15544RIL) having fixed E1, E2, E3, and E4 alleles. Using this approach, we identified three main QTL regions with high logarithm of the odds (LODs), phenotypic variation explained (PVE), and additive effects for maturity and pod-filling within the E8 region: GM04:16,974,874-17,152,230 (E8-r1); GM04:35,168,111-37,664,017 (E8-r2); and GM04:41,808,599-42,376,237 (E8-r3). Using a five-step variant analysis pipeline, we identified Protein far-red elongated hypocotyl 3 (Glyma.04G124300; E8-r1), E1-like-a (Glyma.04G156400; E8-r2), Light-harvesting chlorophyll-protein complex I subunit A4 (Glyma.04G167900; E8-r3), and Cycling dof factor 3 (Glyma.04G168300; E8-r3) as the most promising candidate genes for these regions. A combinatorial eQTL mapping approach identified significant regulatory interactions for 13 expression traits (e-traits), including Glyma.04G050200 (Early flowering 3/E6 locus), with the E8-r3 region. Four other important QTL regions close to or encompassing major flowering genes were also detected on chromosomes GM07, GM08, and GM16. In GM07:5,256,305-5,404,971, a missense polymorphism was detected in the candidate gene Glyma.07G058200 (Protein suppressor of PHYA-105). These findings demonstrate that the locus known as E8 is regulated by at least three distinct genomic regions, all of which comprise major flowering genes.https://www.frontiersin.org/articles/10.3389/fpls.2024.1329065/fullsoybeanGlycine maxearly reproductive traitsgenetic linkage mapquantitative trait lociexpression quantitative trait loci |
| spellingShingle | Jérôme Gélinas Bélanger Jérôme Gélinas Bélanger Tanya Rose Copley Valerio Hoyos-Villegas Louise O’Donoughue Dissection of the E8 locus in two early maturing Canadian soybean populations Frontiers in Plant Science soybean Glycine max early reproductive traits genetic linkage map quantitative trait loci expression quantitative trait loci |
| title | Dissection of the E8 locus in two early maturing Canadian soybean populations |
| title_full | Dissection of the E8 locus in two early maturing Canadian soybean populations |
| title_fullStr | Dissection of the E8 locus in two early maturing Canadian soybean populations |
| title_full_unstemmed | Dissection of the E8 locus in two early maturing Canadian soybean populations |
| title_short | Dissection of the E8 locus in two early maturing Canadian soybean populations |
| title_sort | dissection of the e8 locus in two early maturing canadian soybean populations |
| topic | soybean Glycine max early reproductive traits genetic linkage map quantitative trait loci expression quantitative trait loci |
| url | https://www.frontiersin.org/articles/10.3389/fpls.2024.1329065/full |
| work_keys_str_mv | AT jeromegelinasbelanger dissectionofthee8locusintwoearlymaturingcanadiansoybeanpopulations AT jeromegelinasbelanger dissectionofthee8locusintwoearlymaturingcanadiansoybeanpopulations AT tanyarosecopley dissectionofthee8locusintwoearlymaturingcanadiansoybeanpopulations AT valeriohoyosvillegas dissectionofthee8locusintwoearlymaturingcanadiansoybeanpopulations AT louiseodonoughue dissectionofthee8locusintwoearlymaturingcanadiansoybeanpopulations |