Mapping and validation of a major QTL for primary root length of soybean seedlings grown in hydroponic conditions

Abstract

Background The root system provides nutrient absorption and is closely related to abiotic stress tolerance, but it is difficult to study the roots under field conditions. This study was conducted to identify quantitative trait loci (QTL) associated with primary root length (PRL) during soybean seedling growth in hydroponic conditions. A total of 103 F7 recombinant inbred lines (RILs) derived from a cross between K099 (short primary root) and Fendou 16 (long primary root) were used to identify QTL for PRL in soybean. The RIL population was genotyped with 223 simple sequence repeats markers covering 20 chromosomes. Phenotyping for primary root length was performed for 3-weeks plants grown in hydoponic conditions. The identified QTL was validated in near isogenic lines and in a separate RIL population. Results QTL analysis using inclusive composite interval mapping method identified a major QTL on Gm16 between SSR markers Sat_165 and Satt621, explaining 30.25 % of the total phenotypic variation. The identified QTL, qRL16.1, was further confirmed in a segregating population derived from a residual heterozygous line (RHLs-98). To validate qRL16.1 in a different genetic background, QTL analysis was performed in another F6 RIL population derived from a cross between Union (medium primary root) and Fendou 16, in which a major QTL was detected again in the same genomic region as qRL16.1, explaining 14 % of the total phenotypic variation for PRL. In addition, the effect of qRL16.1 was confirmed using two pair of near-isogenic lines (NILs). PRL was significantly higher in NILs possessing the qRL16.1 allele from Fendou 16 compared to allele from K099. Conclusions The qRL16.1 is a novel QTL for primary root length in soybean which provides important information on the genetic control of root development. Identification of this major QTL will facilitate positional cloning and DNA marker-assisted selection for root traits in soybean.

Genome-Wide Association Study of Root and Shoot Related Traits in Spring Soybean (Glycine max L.) at Seedling Stages Using SLAF-Seq

“…The detected QTLs involved five chromosomes (chromosomes 3, 7, 8, 14, and 20) and harbored various candidate genes. Lately, in a trial using 3-weeks old seedlings derived from a cross between K099 and Fendou16 grown under hydroponic conditions, Chen et al (2021) successfully detected and validated a major QTL associated with primary root length trait located on chromosome 16 between Sat_165 and Satt621 interval markers. Yet, due to low-density markers and large confidence intervals, the localization of these different QTLs was inconsistent among the different findings and further soybean root studies were necessary to detect more chromosomal regions and ultimately identify consistent loci to further screen and identify candidate genes crucial for marker-assisted selection.…”

“…Due to the challenge in achieving reliable root trait data from the field, characterizing crops like soybean with improved root system characteristics in the field remains still a major defy to current plant biology and, root phenotyping studies are commonly conducted under controlled environments ( Rong et al, 2011 ; Seck et al, 2020 ; Chen et al, 2021 ). Besides, some pieces of evidence support that high yielding soybean varieties are supposed to have propitious root systems at the early stages, which may strongly sustain water and nutrients, resulting in increased yield especially under limited water or nutrient availability ( Seck et al, 2020 ; Chen et al, 2021 ; Dayoub et al, 2021 ).…”

“…Due to the challenge in achieving reliable root trait data from the field, characterizing crops like soybean with improved root system characteristics in the field remains still a major defy to current plant biology and, root phenotyping studies are commonly conducted under controlled environments ( Rong et al, 2011 ; Seck et al, 2020 ; Chen et al, 2021 ). Besides, some pieces of evidence support that high yielding soybean varieties are supposed to have propitious root systems at the early stages, which may strongly sustain water and nutrients, resulting in increased yield especially under limited water or nutrient availability ( Seck et al, 2020 ; Chen et al, 2021 ; Dayoub et al, 2021 ). To date, several Quantitative Trait Loci (QTL) studies have been conducted to locate shoot and root-related trait QTLs in soybean under various conditions of growth, at diverse developmental stages and involving various genetic populations ( Rong et al, 2011 ; Brensha et al, 2012 ; Manavalan et al, 2015 ; Prince et al, 2020 ; Seck et al, 2020 ; Chen et al, 2021 ).…”

“…Besides, some pieces of evidence support that high yielding soybean varieties are supposed to have propitious root systems at the early stages, which may strongly sustain water and nutrients, resulting in increased yield especially under limited water or nutrient availability ( Seck et al, 2020 ; Chen et al, 2021 ; Dayoub et al, 2021 ). To date, several Quantitative Trait Loci (QTL) studies have been conducted to locate shoot and root-related trait QTLs in soybean under various conditions of growth, at diverse developmental stages and involving various genetic populations ( Rong et al, 2011 ; Brensha et al, 2012 ; Manavalan et al, 2015 ; Prince et al, 2020 ; Seck et al, 2020 ; Chen et al, 2021 ). Rong et al (2011) in a controlled experiment under hydroponic culture at seedling stage, used a mapping population containing 165 soybean recombinant inbred lines (RILs) derived from the cross between Zhongdou29 and Zhongdou32, and detected 20 QTLs associated with various root and shoot traits located on eight different chromosomes, along with 9 major QTLs on chromosomes 11 and 14.…”

Applications of Molecular Markers for Developing Abiotic-Stress-Resilient Oilseed Crops

“…To date, the majority of research focusing on the identification of QTLs has used small, single populations. Chen et al [ 46 ] discovered QTLs associated with primary root length on chromosome 16 of soybean, which accounts for 30.25% of the variation in phenotype and will help in the development of markers for root-length selection, which is a crucial trait for drought tolerance. In 1996, a research team led by Mian developed an RFLP map in soybean from a population of 120 F 4 -derived lines of a cross ‘Young × PI416937’ that identified the multiple QTLs that are associated with leaf ash and water use efficiency (WUE) [ 47 ].…”