Marker-trait association analysis of frost tolerance of 672 worldwide pea (Pisum sativum L.) collections

Abstract

Frost stress is one of the major abiotic stresses causing seedling death and yield reduction in winter pea. To improve the frost tolerance of pea, field evaluation of frost tolerance was conducted on 672 diverse pea accessions at three locations in Northern China in three growing seasons from 2013 to 2016 and marker-trait association analysis of frost tolerance were performed with 267 informative SSR markers in this study. Sixteen accessions were identified as the most winter-hardy for their ability to survive in all nine field experiments with a mean survival rate of 0.57, ranging from 0.41 to 0.75. Population structure analysis revealed a structured population of two sub-populations plus some admixtures in the 672 accessions. Association analysis detected seven markers that repeatedly had associations with frost tolerance in at least two different environments with two different statistical models. One of the markers is the functional marker EST1109 on LG VI which was predicted to co-localize with a gene involved in the metabolism of glycoproteins in response to chilling stress and may provide a novel mechanism of frost tolerance in pea. These winter-hardy germplasms and frost tolerance associated markers will play a vital role in marker-assisted breeding for winter-hardy pea cultivar.

Genome-wide association study identifies favorable SNP alleles and candidate genes for frost tolerance in pea

“…These 3 QTLs were repeatedly detected in 5, 11 and 10 field conditions for WFD 3.2, WFD 5.1 and WFD 6.1, respectively. Moreover, the position corresponding to WFD 6.1 seems to also match with an EST marker recently found to be associated with frost tolerance in pea [ 38 ]: indeed, Liu et al identified 7 marker-trait associations within a collection of 672 accessions, among which the marker EST1109 was located on LG VI within a functional gene that has a high homology with a gene encoding an alpha-mannosidase in M. truncatula . We reviewed the 1646 transcript-derived SNP markers mapped on LG VI by Tayeh et al [ 36 ] and found that a marker corresponding to an alpha-mannosidase-like protein was located at 43.2 cM on the consensus map; consequently, as the FD-associated markers detected on LG VI in the present study are comprised between 41.4 and 52.8 cM, it is likely that the LG VI positions of both association studies coincide.…”

“…Using the same SNP resource and a collection of 266 pea accessions, including the 175 former lines, Desgroux et al also identified genomic intervals significantly associated with plant architecture and resistance to A. euteiches , of which 8 were overlapping for both traits [ 37 ]. In a different genetic background composed by a set of 672 pea accessions genotyped with 267 simple sequence repeat (SSR) markers, Liu et al [ 38 ] detected 7 SSRs significantly associated with frost tolerance of which one was located on LG VI and was shown to colocalize with a gene involved in the metabolism of glycoproteins in response to chilling stress.…”

Genetic peculiarities and strategy of the pea breeding for the winter sowing

“…У Китаї уже в даний час у субтропічній зоні вирощують, в основному, сорти за підзимового висівання (Liu et al, 2017).…”

“…У другому об'ємному дослідженні китайських вчених 672 колекційних зразків дослідили в 3 зонах впродовж трьох вегетаційних періодів (Liu et al, 2017). В результаті ідентифікували 16 генотипів, які виявились найбільш адаптивними до умов зон дослідження і у 2015-2016 рр.…”

“…Як ми вказували раніше, китайські дослідники ідентифікували ряд зимостійких колекційних сортозразків (Liu et al, 2017). Їх генетичний аналіз із використанням 267 поліморфних маркерів засвідчив значний рівень варіабельності.…”