Identification and confirmation of loci associated with canopy wilting in soybean using genome wide association mapping

Authors: CHAMARTHI, SIVA - University Of Arkansas; KALER, AVJINDER - University Of Arkansas; Abdel-Haleem, Hussein; FRITSCHI, FELIX - University Of Missouri; Gillman, Jason; Ray, Jeffery - Jeff; Smith, James - Rusty; DHANAPAL, ARUN - University Of Missouri; KING, C - University Of Arkansas; PURCELL, LARRAY - University Of Arkansas

Submitted to: Frontiers in Plant Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/14/2021
Publication Date: 7/14/2021
Citation: Chamarthi, S.K., Kaler, A.S., Abdel-Haleem, H.A., Fritschi, F.B., Gillman, J.D., Ray, J.D., Smith, J.R., Dhanapal, A.P., King, C.A., Purcell, L.C. 2021. Identification and confirmation of loci associated with canopy wilting in soybean using genome wide association mapping. Frontiers in Plant Science. 12. Article 698116. https://doi.org/10.3389/fpls.2021.698116.
DOI: https://doi.org/10.3389/fpls.2021.698116

Interpretive Summary: Drought causes significant soybean [Glycine max (L.) Merr.] yield losses each year in rain-fed production systems of many regions. Genetic improvement of soybean for drought tolerance is a cost-effective approach to stabilize yield under rain-fed management. The objectives of the present study were to confirm soybean loci identified previously by genome-wide association mapping and to identify novel loci associated with canopy wilting using a panel of 200 diverse, maturity group (MG) IV accessions. These 200 accessions along with six checks were planted at six site years using an augmented incomplete block design with three replications under irrigated and drought treatments. Association mapping, using 34,680 single nucleotide polymorphisms (SNPs), identified 188 significant SNPs associated with canopy wilting that likely tagged 162 loci. This includes 87 SNPs coincident with previous studies that likely tagged with 68 loci, and 101 novel SNPs that likely tagged 94 loci. We also determined the ability of genomic estimated breeding values (GEBVs) from previous research to predict canopy wilting in different genotypes and environments. A significant positive relationship (P = 0.05; 0.37 = r = 0.50) was observed between observed canopy wilting and GEBVs. Out of 188 significant SNPs, 183 candidate genes were identified from both coincident SNPs and novel SNPs. Among these 183 candidate genes, 57 candidate genes code for proteins having biological functions involved with plant stress responses. These genes may be directly or indirectly associated with transpiration or water conservation. The confirmed genomic regions may be an important resource for pyramiding favorable alleles and also potential candidates for genomic selection to permit improved drought tolerance.

Technical Abstract: Drought causes significant soybean [Glycine max (L.) Merr.] yield losses each year in rain-fed production systems of many regions. Genetic improvement of soybean for drought tolerance is a cost-effective approach to stabilize yield under rain-fed management. The objectives of the present study were to confirm previously reported soybean loci and to identify novel loci associated with canopy wilting using a panel of 200 diverse, maturity group (MG) IV accessions. These 200 accessions along with six checks were planted at six site years using an augmented incomplete block design with three replications under irrigated and rain-fed treatments. Association mapping, using 34,680 single nucleotide polymorphisms (SNPs), identified 188 significant SNPs associated with canopy wilting that likely tagged 152 loci. This includes 87 SNPs coincident with previous studies that likely tagged 68 loci, and 101 novel SNPs that likely tagged 84 loci. We also determined the ability of genomic estimated breeding values (GEBVs) from previous research to predict canopy wilting in different genotypes and environments. A positive relationship (P = 0.05; 0.37 = r = 0.50) was found between observed canopy wilting and GEBVs. In the vicinity of 188 significant SNPs, 183 candidate genes were identified for both coincident SNPs and novel SNPs. Among these 183 candidate genes, 57 SNPs were present within genes coding for proteins with biological functions involved in plant stress responses. These genes may be directly or indirectly associated with transpiration or water conservation. The confirmed genomic regions may be an important resource for pyramiding favorable alleles and as candidates for genomic selection aimed at enhancing soybean drought tolerance.