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

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

doi:10.3389/fpls.2019.00717

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

Front Plant Sci. 2019 Jun 4:10:717. doi: 10.3389/fpls.2019.00717. eCollection 2019.

Authors

Maria Khalid^{1

2}, Fakiha Afzal¹, Alvina Gul¹, Rabia Amir¹, Abid Subhani³, Zubair Ahmed⁴, Zahid Mahmood⁴, Xianchun Xia², Awais Rasheed^{2

5

6}, Zhonghu He^{2

5}

Affiliations

¹ Atta-ur-Rehman School of Applied Biosciences (ASAB), National University of Science and Technology (NUST), Islamabad, Pakistan.
² Institute of Crop Sciences, National Wheat Improvement Centre, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China.
³ Barani Agriculture Research Institute (BARI), Chakwal, Pakistan.
⁴ Crop Science Institute, National Agricultural Research Centre, Islamabad, Pakistan.
⁵ International Maize and Wheat Improvement Centre (CIMMYT), CAAS, Beijing, China.
⁶ Department of Plant Sciences, Quaid-i-Azam University, Islamabad, Pakistan.

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.

Keywords: drought tolerance; functional markers; kompetitive allele-specific PCR markers; marker-trait association; synthetic-derivatives.