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.

Keywords: QTL; SNP; candidate genes; near-isogenic lines; protein; root; wheat.

Figure 1

Contrasting rooting depth of two pairs of wheat near-isogenic lines (NILs) at 42 days after transplanting in a semi-hydroponic system in a glasshouse: (a) rooting depth of a NIL2a (72.8 cm) and a NIL2b (134.2 cm) plant, and (b) a NIL4a (134 cm) and a NIL4b (95.4 cm) plant. The white bar indicates a 40 cm scale.

Figure 2

Structures of candidate genes in the qDSI.4B.1 genomic region (GR). SNP markers are located in different positions of the genes. The genes were identified based on the 90K wheat microarray assessment of near-isogenic lines with contrasting root traits. SNP markers are located in different positions of the genes. Structural information of the genes and SNP markers were obtained from a wheat genome database (https://urgi.versailles.inra.fr/jbrowseiwgsc/gmod_jbrowse/, accessed on 2 March 2021). The measuring bar indicates the DNA length in kilo base pairs (kb).

Figure 2

Structures of candidate genes in the qDSI.4B.1 genomic region (GR). SNP markers are located in different positions of the genes. The genes were identified based on the 90K wheat microarray assessment of near-isogenic lines with contrasting root traits. SNP markers are located in different positions of the genes. Structural information of the genes and SNP markers were obtained from a wheat genome database (https://urgi.versailles.inra.fr/jbrowseiwgsc/gmod_jbrowse/, accessed on 2 March 2021). The measuring bar indicates the DNA length in kilo base pairs (kb).

Figure 3

Structures of candidate genes in the qDT.4A.1 genomic region (GR). SNP markers are located in different positions of the genes. The genes were identified based on the 90K wheat microarray assessment of near-isogenic lines with contrasting root traits. SNP markers are located in different positions of the genes. Structural information of the genes and SNP markers were obtained from wheat genome database (https://urgi.versailles.inra.fr/jbrowseiwgsc/gmod_jbrowse/) (accessed on 2 March 2021). The measuring bar indicates the DNA length in kilo base pairs (kb).

Figure 4

Structures of candidate genes in the QHtscc.ksu-7A genomic region (GR). The genes were identified based on the 90K wheat microarray assessment of near-isogenic lines with contrasting root traits. SNP markers are located in different positions of the genes. Structural information of the genes and SNPs was from a wheat genome database (https://urgi.versailles.inra.fr/jbrowseiwgsc/gmod_jbrowse/, accessed on 2 March 2021). The physical positions of the linking markers of the QTL were found from the original mapping study using parental cultivar; therefore, in the reference genome (Chinese Spring), the QTL extends in both the long and short arm of chromosome 7A, which is unusual. Chromosomal fragment translocation might be the possible reason for the difference between the reference genome and the parental cultivars used in the original mapping study [25]. The measuring bar indicates the DNA length in kilo base pairs (kb).