Identification and validation of two major QTLs for spikelet number per spike in wheat (Triticum aestivum L.)

Xiaoyu Yi; Yingtong Ye; Jinhui Wang; Zhen Li; Jiamin Li; Yuqi Chen; Guoyue Chen; Jian Ma; Zhien Pu; Yuanying Peng; Pengfei Qi; Yaxi Liu; Qiantao Jiang; Jirui Wang; Yuming Wei; Youliang Zheng; Wei Li

doi:10.3389/fpls.2023.1144486

Identification and validation of two major QTLs for spikelet number per spike in wheat (Triticum aestivum L.)

Front Plant Sci. 2023 May 10:14:1144486. doi: 10.3389/fpls.2023.1144486. eCollection 2023.

Authors

Xiaoyu Yi^{1

2

3}, Yingtong Ye^{1

2

3}, Jinhui Wang^{1

2

3}, Zhen Li^{1

2

3}, Jiamin Li^{1

2

3}, Yuqi Chen², Guoyue Chen^{1

3}, Jian Ma^{1

3}, Zhien Pu^{1

2

3}, Yuanying Peng^{1

3}, Pengfei Qi^{1

3}, Yaxi Liu^{1

3}, Qiantao Jiang^{1

3}, Jirui Wang^{1

2}, Yuming Wei^{1

3}, Youliang Zheng^{1

3}, Wei Li^{1

2

3}

Affiliations

¹ State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China.
² College of Agronomy, Sichuan Agricultural University, Chengdu, China.
³ Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China.

Abstract

The total number of spikelets (TSPN) and the number of fertile spikelets (FSPN) affect the final number of grains per spikelet in wheat. This study constructed a high-density genetic map using 55K single nucleotide polymorphism (SNP) arrays from a population of 152 recombinant inbred lines (RIL) from crossing the wheat accessions 10-A and B39. Twenty-four quantitative trait loci (QTLs) for TSPN and 18 QTLs for FSPN were localized based on the phenotype in 10 environments in 2019-2021. Two major QTLs, QTSPN/QFSPN.sicau-2D.4 (34.43-47.43 Mb) and QTSPN/QFSPN.sicau-2D.5(32.97-34.43 Mb), explained 13.97%-45.90% of phenotypic variation. Linked kompetitive allele-specific PCR (KASP) markers further validated these two QTLs and revealed that QTSPN.sicau-2D.4 had less effect on TSPN than QTSPN.sicau-2D.5 in 10-A×BE89 (134 RILs) and 10-A×Chuannong 16 (192 RILs) populations, and one population of Sichuan wheat (233 accessions). The alleles combination haplotype 3 with the allele from 10-A of QTSPN/QFSPN.sicau-2D.5 and the allele from B39 of QTSPN.sicau-2D.4 resulted in the highest number of spikelets. In contrast, the allele from B39 for both loci resulted in the lowest number of spikelets. Using bulk-segregant analysis-exon capture sequencing, six SNP hot spots that included 31 candidate genes were identified in the two QTLs. We identified Ppd-D1a from B39 and Ppd-D1d from 10-A and further analyzed Ppd-D1 variation in wheat. These results identified loci and molecular markers with potential utility for wheat breeding and laid a foundation for further fine mapping and cloning of the two loci.

Keywords: QTL mapping; exon capture trapping; genetic linkage map; genetic localization; multiple spikelets.

Grants and funding

This work is supported by Major Program of National Agricultural Science and Technology of China (NK 20220607), and Sichuan Science and Technology Program (2022ZDZX0014, 2021YFYZ0002), the Applied Basic Research Programs of Science and Technology Department of Sichuan Province (2018JY0020), and the Sichuan Undergraduate Innovation and Entrepreneurship Training Program (S202210626108).