QTL Analysis of Five Morpho-Physiological Traits in Bread Wheat Using Two Mapping Populations Derived from Common Parents

Abstract

Traits such as plant height (PH), juvenile growth habit (GH), heading date (HD), and tiller number are important for both increasing yield potential and improving crop adaptation to climate change. In the present study, these traits were investigated by using the same bi-parental population at early (F2 and F2-derived F3 families) and late (F6 and F7, recombinant inbred lines, RILs) generations to detect quantitative trait loci (QTLs) and search for candidate genes. A total of 176 and 178 lines were genotyped by the wheat Illumina 25K Infinium SNP array. The two genetic maps spanned 2486.97 cM and 3732.84 cM in length, for the F2 and RILs, respectively. QTLs explaining the highest phenotypic variation were found on chromosomes 2B, 2D, 5A, and 7D for HD and GH, whereas those for PH were found on chromosomes 4B and 4D. Several QTL detected in the early generations (i.e., PH and tiller number) were not detected in the late generations as they were due to dominance effects. Some of the identified QTLs co-mapped to well-known adaptive genes (i.e., Ppd-1, Vrn-1, and Rht-1). Other putative candidate genes were identified for each trait, of which PINE1 and PIF4 may be considered new for GH and TTN in wheat. The use of a large F2 mapping population combined with NGS-based genotyping techniques could improve map resolution and allow closer QTL tagging.

Unlocking the molecular basis of wheat straw composition and morphological traits through multi-locus GWAS

“…Plant height plays a crucial role in biomass accumulation and grain yield and all six-multi-locus models identified QTNs associated with this well-studied trait on chromosomes 1A, 2A, 3A, 4B, 5B, 7A, and 7B, consistent with QTLs reported in previous studies [ 33 – 36 ]. Two of them were localized ~ 9 kb far from the main Rht-B1 gene controlling PH trait on chromosome 4B [ 37 ], in the same genomic region where a QTL for the same trait was identified by Vitale et al [ 38 ].…”

High-Density Linkage Mapping of Agronomic Trait QTLs in Wheat under Water Deficit Condition using Genotyping by Sequencing (GBS)

“…This region contains Rht-B1 gene regulating plant height. Previously, QTLs associated with PH, SL, GY and GNS have been reported in this region [ 15 , 17 , 24 , 29 , 33 ]. In the interval of 112–342.7 Mb on 4D, PH QTLs ( Qph-Irr.tab-4D and Qph-Wd.tab-4D ) were mapped with R 2 value ranging from 9.04 to 18.6%.…”

“…To develop drought tolerant varieties it is essential to understand the genetic basis of these complex traits [ 4 ], thus identification of quantitative trait loci (QTL) and genes for important agronomical traits such as grain yield and its components is a key component of crop improvement programs [ 5 ]. To date, a large number of QTLs associated with yield component traits and grain yield under water deficit condition [ 1 , 2 , 3 , 6 , 7 , 8 , 9 , 10 , 11 , 12 , 13 , 14 ] and normal condition [ 15 , 16 , 17 , 18 , 19 , 20 , 21 , 22 , 23 , 24 , 25 , 26 , 27 , 28 , 29 ] have been identified on all 21 wheat chromosomes.…”

Whole-exome sequencing of selected bread wheat recombinant inbred lines as a useful resource for allele mining and bulked segregant analysis

“…Forty-six individuals, derived from the tails of a bi-parental recombinant inbred line population (RIL F6:7 ), previously studied for five high-correlated morpho-physiological traits (i.e., plant height, juvenile growth habit, total tiller number, fertile tiller number and heading date) ( Vitale et al, 2021 ), were analyzed. The population of 176 RILs was developed from a cross between Lankaodali and Rebelde bread wheat cultivars, using the single seed descent method by advancing random F2 plants to the F6:F7 generation ( Vitale et al, 2021 ). The two parental accessions were characterized by contrasting quantitative and qualitative agronomic traits ( Botticella et al, 2018 ; Vitale et al, 2021 ).…”

“…For example, Martinez et al (2020) combined WES with BSA to map ethylmethanesulfonate mutations and identified a novel allele linked to the wheat ERA8 ABA-hypersensitive germination phenotype. Within this motivating context, this study aimed to determine the efficacy of WES for identifying useful alleles within a recombinant inbred line (RIL) population of 46 individuals plus the two parents selected from a previous work in which the entire RIL population was used to identify genomic regions associated with target traits: plant height (PH), juvenile growth habit (GH), heading date (HD), fertile tiller number (FTN) and total tiller number (TTN) ( Vitale et al, 2021 ). We identified many single nucleotide polymorphisms (SNPs) that were classified based on their genomic location and putative biological effect.…”