Root system architecture of historical spring wheat cultivars is associated with alleles and transcripts of major functional genes

Abstract

We evaluated root system architecture (RSA) of a set of 58 historical spring wheat cultivars from Pakistan representing 105 years of selection breeding. The evaluations were carried out under control and water-limited conditions using a high-throughput phenotyping system coupled with RhizoVision Explorer software. The cultivars were classified into three groups based on release year as cultivars released pre-1965, released between 1965 and 2000, and cultivars released post-2000. Under water-limited conditions a decline in 20 out of 25 RSA component traits was observed in pre-1965 cultivars group. Whereas cultivars released after the 1965, so-called green revolution period, showed a decline in 17 traits with significant increments in root length, depth, and steep angle frequency which are important root traits for resource-uptake under water-limited conditions. Similarly, cultivars released after 2000 indicated an increase in the number of roots, depth, diameter, surface area, and steep angle frequency. The coefficient of correlation analysis showed a positive correlation between root depth and yield-related traits under water-limited conditions. We also investigated the effects of green-revolution genes (Rht1) and some phenology-related genes such as DRO1, TaMOR, TaLTPs, TaSus-2B on RSA and identified significant associations of these genes with important root traits. There was strong selection pressure on DRO1 gene in cultivated wheat indicating the allele fixed in modern wheat cultivars is different from landraces. The expression of DRO1, and TaMOR were retrieved from an RNAseq experiment, and results were validated using qRT-PCR. The highest expression of DRO1 and TaMOR was found in Chakwal-50, a rainfed cultivar released in 2008, and MaxiPak-65 released in 1965. We conclude that there is a positive historic change in RSA after 1965 that might be attributed to genetic factors associated with favored RSA traits. Furthermore, we suggest root depth and steep angle as promising traits to withstand water-limited environments and may have implications in selection for breeding.

Genetic Signature Controlling Root System Architecture in Diverse Spring Wheat Germplasm

“…(Beyer et al 2019). In the past, only 58 Pakistan's historical wheat cultivars were evaluated for root architecture system (Maqbool et al 2022a). Therefore, the present study screened the larger Pakistan's landraces and historical wheat cultivars (n = 161) to provide better insight into the prevalence of genetic variations related to RSA.…”

“…Similarly large variations for root traits were observed for large exotic wheat germplasms like n = 323 (Li et al 2019), n = 196 (Xu et al 2021), and n = 201 cultivars representing 200 years of breeding and selection history (Beyer et al 2019). In the past, only 58 Pakistan's historical wheat cultivars were evaluated for root architecture system (Maqbool et al 2022a). Therefore, the present study screened the larger Pakistan's landraces and historical wheat cultivars (n = 161) to provide better insight into the prevalence of genetic variations related to RSA.…”

“…These studies collectively identify the marker-trait associations on chromosomes 1A, 1B, 2A, 2B, 3A, 3B, 5A, 6A, 6B, 6D and 7B. Only one study was performed on Pakistan's wheat historical germplasm (Maqbool et al 2022a) and a lot of germplasms and landraces were unexplored for RSA. The less exploration of this hidden organ is largely due to the complexity of RSA, laborious phenotyping, and difficulty in explaining the root spatial configuration in soil.…”

Genome-wide linkage mapping of root system architecture-related traits in common wheat (Triticum aestivum L.)

“…Optimizing RSA traits is important not only for abiotic stress tolerance but also for efficient nutrient and water acquisition ( Gupta et al., 2017 ; Griffiths et al., 2022 ). RSA traits primarily include root length, surface area, and the number of root tips, which influence the major components and spatial arrangement of root systems, significantly affecting water and nutrient uptake ( Atkinson et al., 2015 ; Maccaferri et al., 2016 ; Liu et al., 2019 ; Li et al., 2020 ; Ma et al., 2022 ; Maqbool et al., 2022 ).…”

“…Previous breeding programs predominantly focused on aboveground traits such as disease resistance, grain quality, and harvest index, while the application of RSA traits has been limited due to the complexity of phenotypic evaluation ( Rogers and Benfey, 2015 ; Roselló et al., 2019 ; Mehrabi et al., 2020 ; Rufo et al., 2020 ; Salarpour et al., 2020 ; Ober et al., 2021 ; Pariyar et al., 2021 ; Saini et al., 2021 ). Previous studies have indicated that the RSA traits are influenced by environmental factors and controlled by minor genes ( Xie et al., 2017 ; Soriano and Alvaro, 2019 ; Maqbool et al., 2022 ). To accelerate the progress of breeding for RSA-related traits, it is imperative to identify the significant associated genomic regions ( Soriano and Alvaro, 2019 ; Yang et al., 2021a ).…”