Genetic diversity and association analysis of leafminer (Liriomyza langei) resistance in spinach (Spinacia oleracea)

Abstract

Leafminer (Liriomyza langei) is a major insect pest of many important agricultural crops, including spinach (Spinacia oleracea). Use of genetic resistance is an efficient, economic, and environment-friendly method to control this pest. The objective of this research was to conduct association analysis and identify single nucleotide polymorphism (SNP) markers associated with leafminer resistance in spinach germplasm. A total of 300 USDA spinach germplasm accessions were used for the association analysis of leafminer resistance. Genotyping by sequencing (GBS) was used for genotyping and 783 SNPs from GBS were used for association analysis. The leafminer resistance showed a near normal distribution with a wide range from 1.1 to 11.7 stings per square centimeter leaf area, suggesting that the leafminer resistance in spinach is a complex trait controlled by multiple genes with minor effect in this spinach panel. Association analysis indicated that five SNP markers, AYZV02040968_7171, AYZV02076752_412, AYZV02098618_4615, AYZV02147304_383, and AYZV02271373_398, were associated with the leafminer resistance with LOD 2.5 or higher. The SNP markers may be useful for breeders to select plants and lines for leafminer resistance in spinach breeding programs through marker-assisted selection.

Genetic diversity and population structure analysis of spinach by single-nucleotide polymorphisms identified through genotyping-by-sequencing

“…spinacia ) resistance in spinach. In previous studies, both two and five structured populations in USDA germplasm accessions were postulated and used in association studied [ 36 – 39 ], similar to the results in this research. In additions, the population structure and phylogeny analysis were also conducted by regions and country in current research.…”

“…For USDA spinach germplasm, we did population structure analysis and had phylogenetic trees among around 300 accessions during our association studies for leafminer ( Liriomyza langei ) resistance [ 36 ], oxalate concentration in leaf [ 37 ], leaf traits [ 38 ], and Stemphylium leaf spot ( Stemphylium botryosum f. sp. spinacia ) [ 39 ] using SNPs from GBS approach and aimed to create the Q-matrix to be used in TASSEL for association analysis.…”

“…spinacia ) [ 39 ] using SNPs from GBS approach and aimed to create the Q-matrix to be used in TASSEL for association analysis. Shi and Mou (2016) [ 36 ] accessed 300 USDA spinach germplasm for their population structure using 783 SNPs from GBS and two structured populations were postulated and used for association analysis of leafminer ( Liriomyza langei ) resistance. Shi et al (2016) [ 37 ] also had two structured populations among 300 USDA spinach germplasm estimated using 841 SNPs for association study in oxalate concentration.…”

Genetic diversity and association mapping of mineral element concentrations in spinach leaves

“…To date, several association studies for different phenotypic traits of spinach have been reported, such as oxalate concentration [ 28 ], leafminer ( Liriomyza spp.) resistance [ 29 ], Verticillium wilt resistance [ 30 ], Stemphylium leaf spot resistance [ 31 ], and leaf traits [ 32 ]. However, no genetic studies have been conducted to evaluate the genetic diversity of mineral elements and no research has been reported regarding mineral elements using association mapping in spinach natural populations to date.…”

Genome Sequences of Spinach Deltapartitivirus 1, Spinach Amalgavirus 1, and Spinach Latent Virus Identified in Spinach Transcriptome

“…In 2014, the world total production of spinach was 24.3 million tons, about 92% of which was produced in China and the USA according to the Food and Agriculture Organization of the United Nations (http://www.fao.org). Breeding programs and genetic studies of spinach have investigated the development of varieties with desirable traits such as increased disease resistance and stress tolerance [1,2]. In addition, comprehensive genomic and transcriptomic studies of spinach have been actively performed to evaluate the genetic diversity of spinach and identify molecular resources, including a comparison of spinach sex chromosomes with sugar beet autosomes [3], a comparative transcriptomic analysis of cultivated and wild spinach varieties [4], and an expression profiling study of spinach leaves under heat stress [5].…”