Identification of Candidate Genes for Root Traits Using Genotype–Phenotype Association Analysis of Near-Isogenic Lines in Hexaploid Wheat (Triticum aestivum L.)

Abstract

Global wheat (Triticum aestivum L.) production is constrained by different biotic and abiotic stresses, which are increasing with climate change. An improved root system is essential for adaptability and sustainable wheat production. In this study, 10 pairs of near-isogenic lines (NILs)—targeting four genomic regions (GRs) on chromosome arms 4BS, 4BL, 4AS, and 7AL of hexaploid wheat—were used to phenotype root traits in a semi-hydroponic system. Seven of the 10 NIL pairs significantly differed between their isolines for 11 root traits. The NIL pairs targeting qDSI.4B.1 GR varied the most, followed by the NIL pair targeting qDT.4A.1 and QHtscc.ksu-7A GRs. For pairs 5–7 targeting qDT.4A.1 GR, pair 6 significantly differed in the most root traits. Of the 4 NIL pairs targeting qDSI.4B.1 GR, pairs 2 and 4 significantly differed in 3 and 4 root traits, respectively. Pairs 9 and 10 targeting QHtscc.ksu-7A GR significantly differed in 1 and 4 root traits, respectively. Using the wheat 90K Illumina iSelect array, we identified 15 putative candidate genes associated with different root traits in the contrasting isolines, in which two UDP-glycosyltransferase (UGT)-encoding genes, TraesCS4A02G185300 and TraesCS4A02G442700, and a leucine-rich repeat receptor-like protein kinase (LRR-RLK)-encoding gene, TraesCS4A02G330900, also showed important functions for root trait control in other crops. This study characterized, for the first time, that these GRs control root traits in wheat, and identified candidate genes, although the candidate genes will need further confirmation and validation for marker-assisted wheat breeding.

Genome-Wide Association Study on Root System Architecture and Identification of Candidate Genes in Wheat (Triticum aestivum L.)

“…To conveniently obtain whole roots, plants were usually cultivated in Hoagland's nutrient solution, sand, or agarose gel [45,54]. Hydroponics is the most common approach used to obtain the whole roots in wheat [22,31,32,42]. Although the QTLs for RSA traits that were identified through hydroponic cultivation coincided with those for yield and nutrient absorption in wheat [43,44,55], we were not sure whether the phenotype of RSA traits in hydroponics was similar to that in soil cultivation.…”

“…6A RGA, NRT, MRL, TRL, ARD, TRA [5,22,23,29,31,[34][35][36]44] 6B RGA, TRL, NRT, MRL, RHL, TRA, ARD, TRV [5,19,[22][23][24]26,29,[34][35][36]39,43] 6D NRT, TRL, TRA, ARD, NRT, MRL, RHL [24,26,28,29,33,34,40,46] 7A RGA, TRL, NRT, TRA, MRL, ARD, TRV [5,[22][23][24][29][30][31][32][33][34][35]37,[39][40][41][42]45] 7B RGA, NRT, TRL, TRA, MRL, ARD, RHL, TRV [5,19,[22][23]…”

Characterization of Root System Architecture Traits in Diverse Soybean Genotypes Using a Semi-Hydroponic System

“…Table 7. Correlation of some important traits (ten root traits and three shoot traits) three soybean genotypes (#054, #055, and #071) between the semi-hydroponic system (39 days after sowing, DAS) and the data from rhizoboxes assessed (a) 38 Data collected in rhizoboxes (81 DAS) were correlated with data for the same traits collected from the semi-hydroponic system, with strong correlations at the 0.01 significance level for root length, shoot height, and root lengths (upper/lower), and at the 0.05 level for hypocotyl length (Table 7b). However, there were no significant correlations for rooting depth, root mass, specific root length, shoot mass, root lengths (coarse), root lengths (fine), or root length ratio (upper/lower), suggesting phenotypic plasticity in these traits at the reproductive stage (Table 7b).…”

“…A semi-hydroponic phenotyping system [31] has been used to characterize root traits in large numbers of germplasm in various crop species, including narrow-leafed lupin (Lupinus angustifolius L.) [32][33][34], chickpea (Cicer arietinum L.) [35], maize (Zea mays L.) [36], wheat (Triticum aestivum L.) [37,38], and barley (Hordeum vulgare L.) [39], but not in soybean. In this study, we characterized phenotypic variability in root morphology at the seedling stage of the 171 diverse genotypes with good agronomic traits mainly developed for the Yangtze and Huaihe Rivers in eastern China.…”

Wheat Proteomics for Abiotic Stress Tolerance and Root System Architecture: Current Status and Future Prospects

“…It exhibits a specific spatial and temporal configuration of different root types [ 11 ]. RSA is the primary plant part to supply nutrients and water from the soil, and good anchorage in any environmental condition [ 12 , 13 ]. Therefore, RSA plays a key role in ensuring sustainable yields under different environmental scenarios.…”