Molecular Characterization of 87 Functional Genes in Wheat Diversity Panel and Their Association With Phenotypes Under Well-Watered and Water-Limited Conditions.

Maria Khalid,Zhonghu He,Rabia Amir,Awais Rasheed,Alvina Gul,Zahid Mahmood,Fakiha Afzal,Xianchun Xia,Abid Subhani,Zubair Ahmed

doi:10.3389/fpls.2019.00717

Abstract

Modern breeding imposed selection for improved productivity that largely influenced the frequency of superior alleles underpinning traits of breeding interest. Therefore, molecular diagnosis for the allelic variations of such genes is important to manipulate beneficial alleles in wheat molecular breeding. We analyzed a diversity panel largely consisted of advanced lines derived from synthetic hexaploid wheats for allelic variation at 87 functional genes or loci of breeding importance using 124 high-throughput KASP markers. We also developed two KASP markers for water-soluble carbohydrate genes (TaSST-D1 and TaSST-A1) associated with plant height and thousand grain weight (TGW) in the diversity panel. KASP genotyping results indicated that beneficial alleles for genes underpinning flowering time (Ppd-D1 and Vrn-D3), thousand grain weight (TaCKX-D1, TaTGW6-A1, TaSus1-7B, and TaCwi-D1), water-soluble carbohydrates (TaSST-A1), yellow-pigment content (Psy-B1 and Zds-D1), and root lesion nematodes (Rlnn1) were fixed in diversity panel with frequency ranged from 96.4 to 100%. The association analysis of functional genes with agronomic and biochemical traits under well-watered (WW) and water-limited (WL) conditions revealed that 21 marker-trait associations (MTAs) were consistently detected in both moisture conditions. The major developmental genes such as Vrn-A1, Rht-D1, and Ppd-B1 had the confounding effect on several agronomic traits including plant height, grain size and weight, and grain yield in both WW and WL conditions. The accumulation of favorable alleles for grain size and weight genes additively enhanced grain weight in the diversity panel. Graphical genotyping approach was used to identify accessions with maximum number of favorable alleles, thus likely to have high breeding value. These results improved our knowledge on the selection of favorable and unfavorable alleles through unconscious selection breeding and identified the opportunities to deploy alleles with effects in wheat breeding.

Highlights

Insight into genetic loci that have been selected during modern wheat breeding is of significant importance to understand the phenotypic variation in modern wheat cultivars
A diversity panel of 213 advanced lines derived from synthetic hexaploid wheats (SHWs) and elite bread wheat cultivars was used in the present study (Supplementary Table S1), comprising
DNA was extracted from all genotypes using a modified CTAB method (Dreisigacker et al, 2013)

Summary

Introduction

Insight into genetic loci that have been selected during modern wheat breeding is of significant importance to understand the phenotypic variation in modern wheat cultivars. This will enable wheat breeding to transit to knowledge-based activity and will improve the rate of genetic progress in wheat (Li H. et al, 2018). More than 150 functional markers are available for important genes in wheat (Liu et al, 2012), and were subsequently converted into high-throughput KASP assays (Rasheed et al, 2016a) Such as, genes related to grain size and weight (Nadolska-Orczyk et al, 2017), developmental traits like photoperiod response and vernalization (Kamran et al, 2014), and end-use quality. Genes for grain size and weight including TaTGW6 (Hanif et al, 2015; Hu et al, 2016), TaCwi-A1 (Ma et al, 2012), TaSus2-2B (Jiang et al, 2011), TaSus2-2A, TaSus1-7A (Hou et al, 2014), TaGW2-6A, 6B (Su et al, 2011; Yang et al, 2012; Qin et al, 2014), TaCKX6-D1 (Zhang et al, 2012), TaSAP1-A1 (Chang et al, 2013), TaGS-D1 (Zhang et al, 2014; Ma et al, 2016), and TaGASR-A1 (Dong et al, 2014) have been cloned in wheat using comparative genomics approaches

Methods

Results

Conclusion