AUTHOR=Gélinas Bélanger Jérôme , Copley Tanya Rose , Hoyos-Villegas Valerio , O’Donoughue Louise 

TITLE=Dissection of the E8 locus in two early maturing Canadian soybean populations

JOURNAL=Frontiers in Plant Science

VOLUME=15

YEAR=2024

URL=https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2024.1329065

DOI=10.3389/fpls.2024.1329065

ISSN=1664-462X

ABSTRACT=<p>Soybean [<italic>Glycine max</italic> (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 <italic>E8</italic> 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 (QS15524<sub>F2:F3</sub> and QS15544<sub>RIL</sub>) having fixed <italic>E1</italic>, <italic>E2</italic>, <italic>E3</italic>, and <italic>E4</italic> 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 <italic>E8</italic> region: GM04:16,974,874-17,152,230 (<italic>E8-r1</italic>); GM04:35,168,111-37,664,017 (<italic>E8-r2</italic>); and GM04:41,808,599-42,376,237 (<italic>E8-r3</italic>). Using a five-step variant analysis pipeline, we identified <italic>Protein far-red elongated hypocotyl 3</italic> (<italic>Glyma.04G124300</italic>; <italic>E8-r1</italic>), <italic>E1-like-a</italic> (<italic>Glyma.04G156400</italic>; <italic>E8-r2</italic>), <italic>Light-harvesting chlorophyll-protein complex I subunit A4</italic> (<italic>Glyma.04G167900</italic>; <italic>E8-r3</italic>), and <italic>Cycling dof factor 3</italic> (<italic>Glyma.04G168300</italic>; <italic>E8-r3</italic>) 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 <italic>Glyma.04G050200</italic> (<italic>Early flowering 3/E6</italic> locus), with the <italic>E8-r3</italic> 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 <italic>Glyma.07G058200</italic> (<italic>Protein suppressor of PHYA-105</italic>). These findings demonstrate that the locus known as <italic>E8</italic> is regulated by at least three distinct genomic regions, all of which comprise major flowering genes.</p>