Assessment of the genetic diversity and population structure of groundnut germplasm collections using phenotypic traits and SNP markers: Implications for drought tolerance breeding

Abady, Seltene; Shimelis, Hussein; Janila, Pasupuleti; Shasidhar, Yaduru; Shayanowako, Admire; Deshmukh, Dnyaneshwar B.; Chaudhari, Sunil; Manohar, Surendra S.

doi:10.1371/journal.pone.0259883

Cited by 15 publications

(10 citation statements)

References 53 publications

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“…Based on 3,474 SNPs, the genetic diversity of these 31 accessions was investigated using several approaches. As a whole, this panel has an average PIC, expected He, MAF and genetic distance of 0.16, 0.19, 0.86, 0.17, respectively, which is concordant with previous research using SNP genotyping 39,40,41 . In terms of the marker polymorphism, the PIC value is an indicator of markers that can reveal polymorphisms.…”

Section: Discussionsupporting

confidence: 90%

“…The average PIC of 0.16 from these 31 accessions falls in this last class, while 32% of the identified SNPs correspond to the reasonably informative class. In studies of other germplasm collections, the mean PIC value ranged from 0.08 to 0.26 even though some of these collections had a mixture of four market-type accessions including the U.S. Peanut mini core collection 39,40,41 , implying that the germplasm panel of 31 accessions chosen in this study preserves a high proportion of overall genetic diversity in spite of a smaller sample size. Concerning the origin of our germplasm, the global subset (n = 17) has a higher average PIC value (0.15) than the local subset (0.13 with n = 14).…”

Section: Discussionmentioning

confidence: 88%

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Assessment of genetic diversity and SNP marker development within peanut germplasm in Taiwan by RAD-seq

Hsu

Wang²,

Tseng

et al. 2022

Preprint

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The cultivated peanut (Arachis hypogaea L.) is an important oil crop but has a narrow genetic diversity. Molecular markers can be used to probe the genetic diversity of various germplasm. In this study, the restriction site associated DNA (RAD) approach was utilized to sequence 31 accessions of Taiwanese peanut germplasm, leading to the identification of a total of 17,610 single nucleotide polymorphisms (SNPs). The origin of these 31 accessions is contrasted so the global subset (n = 17) has greater genetic diversity than the local subset (n = 14). Concerning botanical varieties, the var. fastigiata subset has greater genetic diversity than the other two subsets of var. vulgaris and var. hypogaea, suggesting that novel genetic resources should be introduced into breeding programs to enhance genetic diversity. Principal component analysis (PCA) using genotyping data separated the 31 accessions into three clusters largely according to the botanical varieties, consistent with the PCA result for 282 accessions genotyped by 14 kompetitive allele-specific PCR (KASP) markers developed in this study. The SNP markers identified in this work not only revealed the genetic relationship and population structure of current germplasm in Taiwan, but also offer an efficient tool for breeding and further genetic applications.

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Section: Discussionsupporting

confidence: 90%

Section: Discussionmentioning

confidence: 88%

Assessment of genetic diversity and SNP marker development within peanut germplasm in Taiwan by RAD-seq

Hsu

Wang²,

Tseng

et al. 2022

Preprint

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“…The characteristics and uses of some of the most popular peanut varieties has been detailed by many authors [ 34 , 36 , 37 , 38 , 39 , 40 , 41 ]. Table 1 shows some of the most popular peanut varieties, their general characteristics, and their uses.…”

Section: Peanut Varieties and Cultivarsmentioning

confidence: 99%

“…In addition, to complement conventional breeding programs, significant advances have been made in the utilization of genomic tools for high-resolution trait mapping using germplasm diversity panels and data from multi-parent genetic populations [ 48 ]. The use of genomic tools has greatly increased the precision and speed at which new peanut breeds with targeted desirable traits are developed and brought onto the market, while circumventing the confounding effects of environmental conditions that are normally encountered in conventional breeding [ 33 , 41 , 48 ]. Using these recent technological advances, several research studies have been carried out with the aim of amplifying the expression of some desirable traits in peanuts [ 30 , 41 , 49 , 50 , 51 ].…”

Section: Peanut Varieties and Cultivarsmentioning

confidence: 99%

Influence of Peanut Varieties on the Sensory Quality of Peanut Butter

Sithole

Qin

et al. 2022

Foods

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Over the years, concentrated efforts have been directed toward the improvement of desirable characteristics and attributes in peanut cultivars. Most of these breed improvement programs have been targeting attributes that involve peanut growth, productivity, drought and disease tolerance, and oil quality and content, with only a few articles focusing directly on improvements in peanut butter organoleptic qualities. There are numerous peanut cultivars on the market today, with widely differing chemical compositions and metabolite profiles, about which little is known concerning their suitability for making peanut butter. In this review, we detail how the numerous peanut varieties on the market today, with their genetically conferred physiochemical attributes, can significantly affect the sensory quality attributes of peanut butter, even in peanut butter processing lines with optimized processes. If other peanut butter processing parameters are held constant, variations in the chemical composition and metabolite profiles of peanuts have a significant impact on peanut butter color, flavor, texture, storage stability, shelf life, and overall product acceptance by consumers. Further research on breeding programs for peanut varieties that are specifically tailored for peanut butter production, and even more comprehensive research on the synergetic relationship between peanut chemical composition and peanut butter organoleptic quality, are still required.

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“…The geographic pattern and distribution of plants across complex habitats have been extensively studied and well-documented (Martyn, 1729 ; Bradshaw, 1965 ; Crisci, 2001 ). The cellular and mechanistic processes responsible for the adaptive potential and phenotypic plasticity of plants are still largely undefined but thought to involve processes exclusive to the plant's genome and considered as the primary factor responsible for plant distribution patterns and biogeography (Chevin et al, 2010 ; Matesanz et al, 2010 ; Nicotra et al, 2010 ; Zhang et al, 2013 ; Gratani, 2014 ; Zhou et al, 2019 ; Liu et al, 2020 ; Monforte, 2020 ; Abady et al, 2021 ; Klupczyńska and Ratajczak, 2021 ; Stotz et al, 2021 ; Syngelaki et al, 2021 ; Yang et al, 2021 ; Yu et al, 2021 ; Wang et al, 2022 ). For example, some plants are adapted to the presence of selenium enabling them to grow in soils with high concentrations of the element that limit the distribution of the plant's competitors (El Mehdawi et al, 2011a , b ).…”

Section: Introductionmentioning

confidence: 99%

Symbiotic Modulation as a Driver of Niche Expansion of Coastal Plants in the San Juan Archipelago of Washington State

et al. 2022

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Modern evolutionary theory and population genetics posit that adaptation and habitat expansion of plants result from processes exclusive to their genomes. Here, we present studies showing that plants can grow across complex habitat gradients by modulating symbiotic associations with Class 2 fungal endophytes. Endophyte analysis of three native (Leymus mollis, Distichlis spicata, and Salicornia pacifica) and one invasive (Spartina anglica) plant growing across adjacent microhabitats in the San Juan Archipelago altered associations with Class 2 fungal endophytes in response to soil salinity levels. At the microhabitat interfaces where the gradation of salinity varied, the plants were colonized by endophytes from both microhabitats. A reciprocal transplant study along a salt gradient demonstrated that Leymus mollis (dunegrass) required endophytes indigenous to each microhabitat for optimal fitness and/or survival. In contrast, when dunegrass and Grindelia integrifolia (gumweed) were found growing in low salinity, but high drought habitats, these plant species had their own unique dominant endophyte association regardless of geographic proximity and conferred drought but not high salt stress tolerance. Modulation of endophyte abundance occurred in planta based on the ability of the symbiont to confer tolerance to the stress imposed on plants. The ability of an endophyte to confer appropriate stress tolerance resulted in a significant increase of in planta fungal abundance. Conversely, the inability of an endophyte to confer stress tolerance resulted in a decrease of in planta fungal abundance. Our studies indicate that Class 2 fungal endophytes can provide a symbiotic mechanism for niche expansion and phenotypic plasticity across environmental gradients.

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Assessment of the genetic diversity and population structure of groundnut germplasm collections using phenotypic traits and SNP markers: Implications for drought tolerance breeding

Cited by 15 publications

References 53 publications

Assessment of genetic diversity and SNP marker development within peanut germplasm in Taiwan by RAD-seq

Assessment of genetic diversity and SNP marker development within peanut germplasm in Taiwan by RAD-seq

Influence of Peanut Varieties on the Sensory Quality of Peanut Butter

Symbiotic Modulation as a Driver of Niche Expansion of Coastal Plants in the San Juan Archipelago of Washington State

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