Genome-Wide Association Study of Leaf Chlorophyll Content Using High-Density SNP Array in Peanuts (Arachis hypogaea L.)

Zou, Kunyan; Kim, Ki-Seung; Kang, Dong-Woo; Kim, Min‐Cheol; Ha, Jung Min; Moon, Jung‐Kyung; Jun, Tae-Hwan

doi:10.3390/agronomy12010152

Cited by 5 publications

(3 citation statements)

References 65 publications

(71 reference statements)

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“…Previous studies have successfully identified loci significantly associated with chlorophyll or anthocyanin in the leaves or petals of various plants, such as tea plant ( Camellia spp. Kamel) [ 23 ], peanut ( Arachis hypogaea L.) [ 24 ], rose ( Rosa rugosa Thunb.) [ 25 ], Gerbera hybrida [ 20 ], rice ( Oryza sativa L.) [ 26 , 27 , 28 ], and Perilla frutescens (L.) Britt.…”

Section: Discussionmentioning

confidence: 99%

Pigment Diversity in Leaves of Caladium × hortulanum Birdsey and Transcriptomic and Metabolic Comparisons between Red and White Leaves

Zhou,

Xu,

Zhu

et al. 2024

IJMS

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Leaf color is a key ornamental characteristic of cultivated caladium (Caladium × hortulanum Birdsey), a plant with diverse leaf colors. However, the genetic improvement of leaf color in cultivated caladium is hindered by the limited understanding of leaf color diversity and regulation. In this study, the chlorophyll and anthocyanin content of 137 germplasm resources were measured to explore the diversity and mechanism of leaf color formation in cultivated caladium. Association analysis of EST-SSR markers and pigment traits was performed, as well as metabolomics and transcriptomics analysis of a red leaf variety and its white leaf mutant. We found significant differences in chlorophyll and anthocyanin content among different color groups of cultivated caladium, and identified three, eight, three, and seven EST-SSR loci significantly associated with chlorophyll-a, chlorophyll-b, total chlorophyll and total anthocyanins content, respectively. The results further revealed that the white leaf mutation was caused by the down-regulation of various anthocyanins (such as cyanidin-3-O-rutinoside, quercetin-3-O-glucoside, and others). This change in concentration is likely due to the down-regulation of key genes (four PAL, four CHS, six CHI, eight F3H, one F3′H, one FLS, one LAR, four DFR, one ANS and two UFGT) involved in anthocyanin biosynthesis. Concurrently, the up-regulation of certain genes (one FLS and one LAR) that divert the anthocyanin precursors to other pathways was noted. Additionally, a significant change in the expression of numerous transcription factors (12 NAC, 12 bZIP, 23 ERF, 23 bHLH, 19 MYB_related, etc.) was observed. These results revealed the genetic and metabolic basis of leaf color diversity and change in cultivated caladium, and provided valuable information for molecular marker-assisted selection and breeding of leaf color in this ornamental plant.

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Section: Discussionmentioning

confidence: 99%

Pigment Diversity in Leaves of Caladium × hortulanum Birdsey and Transcriptomic and Metabolic Comparisons between Red and White Leaves

Zhou,

Xu,

Zhu

et al. 2024

IJMS

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“…The gene Arahy. SDG4EV was found to be related to leaf chlorophyll content ( Zou et al, 2022 ). The chlorophyll content is a critical component affecting photosynthesis in plants and is associated with abiotic stress adaptation ( Singh and Thakur, 2018 ).…”

Section: Molecular Basis Of Stress Tolerancementioning

confidence: 99%

Sustaining yield and nutritional quality of peanuts in harsh environments: Physiological and molecular basis of drought and heat stress tolerance

et al. 2023

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Climate change is significantly impacting agricultural production worldwide. Peanuts provide food and nutritional security to millions of people across the globe because of its high nutritive values. Drought and heat stress alone or in combination cause substantial yield losses to peanut production. The stress, in addition, adversely impact nutritional quality. Peanuts exposed to drought stress at reproductive stage are prone to aflatoxin contamination, which imposes a restriction on use of peanuts as health food and also adversely impact peanut trade. A comprehensive understanding of the impact of drought and heat stress at physiological and molecular levels may accelerate the development of stress tolerant productive peanut cultivars adapted to a given production system. Significant progress has been achieved towards the characterization of germplasm for drought and heat stress tolerance, unlocking the physiological and molecular basis of stress tolerance, identifying significant marker-trait associations as well major QTLs and candidate genes associated with drought tolerance, which after validation may be deployed to initiate marker-assisted breeding for abiotic stress adaptation in peanut. The proof of concept about the use of transgenic technology to add value to peanuts has been demonstrated. Advances in phenomics and artificial intelligence to accelerate the timely and cost-effective collection of phenotyping data in large germplasm/breeding populations have also been discussed. Greater focus is needed to accelerate research on heat stress tolerance in peanut. A suits of technological innovations are now available in the breeders toolbox to enhance productivity and nutritional quality of peanuts in harsh environments. A holistic breeding approach that considers drought and heat-tolerant traits to simultaneously address both stresses could be a successful strategy to produce climate-resilient peanut genotypes with improved nutritional quality.

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“…The development of high-density SNP chips in groundnut allowed the construction of high-density genetic maps that helped to saturate the large QTL intervals ( Pandey et al, 2017b ). SNP arrays were successfully used to dissect the yield-related traits ( Pandey et al, 2020b ), root-knot nematode resistance ( Ballén-Taborda et al, 2019 ), stem rot resistance ( Luo et al, 2020 ), late leaf spot resistance ( Han et al, 2018 ; Chu et al, 2019 ; Zhang et al, 2020 ), fresh seed dormancy ( Wang et al, 2022 ), leaf chlorophyll content ( Zou et al, 2022 ), salinity tolerance ( Zou et al, 2020a ), background genome recovery during a marker-assisted backcross selection in groundnut ( Shasidhar et al, 2020 ), and germplasm diversity analysis ( Nabi et al, 2021 ). Specific locus amplified fragment sequencing (SLAF-seq)-based high-density genetic map and phenotyping under multiple environments identified a total of 27 QTLs for seed weight, seed length, and width ( Zhang et al, 2019 ).…”

Section: Introductionmentioning

confidence: 99%

Genetic mapping identifies genomic regions and candidate genes for seed weight and shelling percentage in groundnut

et al. 2023

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Seed size is not only a yield-related trait but also an important measure to determine the commercial value of groundnut in the international market. For instance, small size is preferred in oil production, whereas large-sized seeds are preferred in confectioneries. In order to identify the genomic regions associated with 100-seed weight (HSW) and shelling percentage (SHP), the recombinant inbred line (RIL) population (Chico × ICGV 02251) of 352 individuals was phenotyped for three seasons and genotyped with an Axiom_Arachis array containing 58K SNPs. A genetic map with 4199 SNP loci was constructed, spanning a map distance of 2708.36 cM. QTL analysis identified six QTLs for SHP, with three consistent QTLs on chromosomes A05, A08, and B10. Similarly, for HSW, seven QTLs located on chromosomes A01, A02, A04, A10, B05, B06, and B09 were identified. BIG SEED locus and spermidine synthase candidate genes associated with seed weight were identified in the QTL region on chromosome B09. Laccase, fibre protein, lipid transfer protein, senescence-associated protein, and disease-resistant NBS-LRR proteins were identified in the QTL regions associated with shelling percentage. The associated markers for major-effect QTLs for both traits successfully distinguished between the small- and large-seeded RILs. QTLs identified for HSW and SHP can be used for developing potential selectable markers to improve the cultivars with desired seed size and shelling percentage to meet the demands of confectionery industries.

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Genome-Wide Association Study of Leaf Chlorophyll Content Using High-Density SNP Array in Peanuts (Arachis hypogaea L.)

Cited by 5 publications

References 65 publications

Pigment Diversity in Leaves of Caladium × hortulanum Birdsey and Transcriptomic and Metabolic Comparisons between Red and White Leaves

Pigment Diversity in Leaves of Caladium × hortulanum Birdsey and Transcriptomic and Metabolic Comparisons between Red and White Leaves

Sustaining yield and nutritional quality of peanuts in harsh environments: Physiological and molecular basis of drought and heat stress tolerance

Genetic mapping identifies genomic regions and candidate genes for seed weight and shelling percentage in groundnut

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