Identification of novel loci associated with maturity and yield traits in early maturity soybean plant introduction lines

Abstract Background To continue to meet the increasing demands of soybean worldwide, it is crucial to identify key genes regulating flowering and maturity to expand the cultivated regions into short season areas. Although four soybean genes have been successfully utilized in early maturity breeding programs, new genes governing maturity are continuously being identified suggesting that there remains as yet undiscovered loci governing agronomic traits of interest. The objective of this study was to identify novel loci and genes involved in a diverse set of early soybean maturity using genome-wide association (GWA) analyses to identify loci governing days to maturity (DTM), flowering (DTF) and pod filling (DTPF), as well as yield and 100 seed weight in Canadian environments. To do so, soybean plant introduction lines varying significantly for maturity, but classified as early varieties, were used. Plants were phenotyped for the five agronomic traits for five site-years and GWA approaches used to identify candidate loci and genes affecting each trait. Results Genotyping using genotyping-by-sequencing and microarray methods identified 67,594 single nucleotide polymorphisms, of which 31,283 had a linkage disequilibrium  0.05 and were used for GWA analyses. A total of 9, 6, 4, 5 and 2 loci were detected for GWA analyses for DTM, DTF, DTPF, 100 seed weight and yield, respectively. Regions of interest, including a region surrounding the E1 gene for flowering and maturity, and several novel loci, were identified, with several loci having pleiotropic effects. Novel loci affecting maturity were identified on chromosomes five and 13 and reduced maturity by 7.2 and 3.3 days, respectively. Novel loci for maturity and flowering contained genes orthologous to known Arabidopsis flowering genes, while loci affecting yield and 100 seed weight contained genes known to cause dwarfism. Conclusions This study demonstrated substantial variation in soybean agronomic traits of interest, including maturity and flowering dates as well as yield, and the utility of GWA analyses in identifying novel genetic factors underlying important agronomic traits. The loci and candidate genes identified serve as promising targets for future studies examining the mechanisms underlying the related soybean traits

Image_1_Dissection of the E8 locus in two early maturing Canadian soybean populations.jpeg

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.</p

Table_1_Dissection of the E8 locus in two early maturing Canadian soybean populations.xlsx

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.</p

Évaluation de maladies racinaires du soya dans des champs de la Montérégie en 2014 et 2015

Un inventaire des maladies racinaires du soya causées par des champignons et des oomycètes a été réalisé en 2014 et 2015 dans 80 champs situés en Montérégie et 4 au Centre-du-Québec. Douze plantules au stade de deux feuilles trifoliées ont été prélevées par champ pour évaluer l’état sanitaire de leurs racines (indice racinaire) selon une échelle de 1 à 5 (1 = belles racines abondantes ; 5 = nécroses et peu de racines), et pour révéler dans ces racines, à l’aide de techniques de mise en culture, la présence de champignons et d’oomycètes pathogènes. L’indice racinaire moyen pour l’ensemble des champs était de 2,6 en 2014 et 3,2 en 2015. Des espèces de Pythium et de Fusarium étaient présentes dans presque 100 % des champs chaque année, alors que Rhizoctonia solani et Thielaviopsis basicola ont été plus abondants en 2015 (88 % des champs) qu’en 2014 (52 %). Phytophthora sojae n’a été isolé d’aucune racine, mais l’a été à partir des sols de 37 % des champs. Les espèces de Fusarium les plus fréquentes étaient F. solani, F. oxysporum et F. equiseti, présentes dans au moins 60 % des champs. La méthode d’analyse « stepwise » a sélectionné trois facteurs pour expliquer la variation de l’indice racinaire, dont deux ont montré des différences significatives entre leurs niveaux, soit le type de semence (indice plus élevé pour non-OGM que pour OGM) et le nombre d’années en culture de soya au cours des quatre dernières années (indice augmentant avec le nombre d’années). Le travail du sol a été le seul facteur sélectionné pour expliquer la variation des Fusarium totaux (somme diminuant avec l’intensité du travail de sol).A survey on soybean root diseases caused by fungi and oomycetes was conducted in 2014 and 2015 in 80 fields in Montérégie and 4 fields in Centre-du-Québec. Twelve seedlings at two-trifoliate-leaf stage were collected per field to assess their root health (root index) on a scale of 1 to 5 (1 = healthy abundant roots, 5 = necrosis and few roots), and to reveal in theses roots, by plating techniques, the presence of pathogenic fungi and oomycetes. The average root index for all fields was 2.6 in 2014 and 3.2 in 2015. Pythium and Fusarium species were present in almost 100% of the fields each year, while Rhizoctonia solani and Thielaviopsis basicola were more abundant in 2015 (88% of the fields) than in 2014 (52%). Phytophthora sojae was not isolated from any root, but was isolated from soils in 37% of the fields. The most common Fusarium species were F. solani, F. oxysporum and F. equiseti, found in at least 60% of the fields. The stepwise-analysis method selected three factors to explain the variation of root index, two of which showed significant differences between their levels, namely the type of seeds (higher index for non-GMOs than for GMOs). and the number of years in soybean crop over the past four years (index increasing with the number of years). Tillage was the only factor selected to explain the variation of the sum of Fusarium isolates (sum decreasing with the intensity of tillage)