Fine-Mapping of a Wild Genomic Region Involved in Pod and Seed Size Reduction on Chromosome A07 in Peanut (Arachis hypogaea L.)

Alyr, Mounirou Hachim; Pallu, Justine; Sambou, Aissatou; Nguepjop, Joël Romaric; Seye, Maguette; Tossim, Hodo-Abalo; Djiboune, Yvette R.; Sané, Djibril; Rami, Jean-François; Foncéka, Daniel

doi:10.3390/genes11121402

Cited by 23 publications

(28 citation statements)

References 65 publications

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“…Several major quantitative trait loci (QTLs) related to peanut pod size have been reported in recent years ( Huang et al, 2015 ; Chen et al, 2016 ; Luo et al, 2017 ; Luo et al, 2018 ; Alyr et al, 2020 ; Chu et al, 2020 ; Gangurde et al, 2020 ). Luo et al (2017) identified three major QTLs for hundred-pod weight (HPW), pod length and width (PL and PW), which were co-localized in the same region on chromosome A05.…”

Section: Introductionmentioning

confidence: 99%

“… Chu et al (2020) identified one major QTL for pod-related traits in a 9 Mbp interval on linkage group A05. Alyr et al (2020) identified one QTL associated with pod and seed size in a 168.37 kb interval on chromosome A07. Gangurde et al (2020) identified 44 major effect QTLs related to PW and SW in two nested-association mapping populations, and found that most of the QTLs distributed on chromosomes A05, A06, B05, and B06.…”

Section: Introductionmentioning

confidence: 99%

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Transcriptome analysis of pod mutant reveals plant hormones are important regulators in controlling pod size in peanut (Arachis hypogaea L.)

Wang

Zhang

et al. 2022

PeerJ

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Pod size is an important yield-influencing trait in peanuts. It is affected by plant hormones and identifying the genes related to these hormones may contribute to pod-related trait improvements in peanut breeding programs. However, there is limited information on the molecular mechanisms of plant hormones that regulate pod size in peanuts. We identified a mutant with an extremely small pod (spm) from Yuanza 9102 (WT) by 60Co γ-radiation mutagenesis. The length and width of the natural mature pod in spm were only 71.34% and 73.36% of those in WT, respectively. We performed comparative analyses for morphological characteristics, anatomy, physiology, and global transcriptome between spm and WT pods. Samples were collected at 10, 20, and 30 days after peg elongation into the soil, representing stages S1, S2, and S3, respectively. The differences in pod size between WT and spm were seen at stage S1 and became even more striking at stages S2 and S3. The cell sizes of the pods were significantly smaller in spm than in WT at stages S1, S2, and S3. These results suggested that reduced cell size may be one of the important contributors for the small pod in spm. The contents of indole-3-acetic acid (IAA), gibberellin (GA), and brassinosteroid (BR) were also significantly lower in spm pods than those in WT pods at all three stages. RNA-Seq analyses showed that 1,373, 8,053, and 3,358 differently expressed genes (DEGs) were identified at stages S1, S2, and S3, respectively. Functional analyses revealed that a set of DEGs was related to plant hormone biosynthesis, plant hormone signal transduction pathway, and cell wall biosynthesis and metabolism. Furthermore, several hub genes associated with plant hormone biosynthesis and signal transduction pathways were identified through weighted gene co-expression network analysis. Our results revealed that IAA, GA, and BR may be important regulators in controlling pod size by regulating cell size in peanuts. This study provides helpful information for the understanding of the complex mechanisms of plant hormones in controlling pod size by regulating the cell size in peanuts and will facilitate the improvement of peanut breeding.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Transcriptome analysis of pod mutant reveals plant hormones are important regulators in controlling pod size in peanut (Arachis hypogaea L.)

Wang

Zhang

et al. 2022

PeerJ

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“…Thus, as the demand for oil is ever-increasing, there is an urgent need to breed new peanut varieties with high yields, a characteristic that is dependent on seed size. Several major quantitative trait loci (QTLs) related to peanut pod size have been obtained in recent years [ 12 , 25 , 26 , 27 , 28 , 29 , 30 , 31 ]. Luo and colleagues found three major consistent and stable QTLs for pod size and weight, which were co-localized in a 3.7 cm interval on chromosome A05 [ 27 ].…”

Section: Discussionmentioning

confidence: 99%

Multi-Omics Profiling Identifies Candidate Genes Controlling Seed Size in Peanut

Liu

et al. 2022

Plants

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Seed size is the major yield component and a key target trait that is selected during peanut breeding. However, the mechanisms that regulate peanut seed size are unknown. Two peanut mutants with bigger seed size were isolated in this study by 60Co treatment of a common peanut landrace, Huayu 22, and were designated as the “big seed” mutant lines (hybs). The length and weight of the seed in hybs were about 118% and 170% of those in wild-type (WT), respectively. We adopted a multi-omics approach to identify the genomic locus underlying the hybs mutants. We performed whole genome sequencing (WGS) of WT and hybs mutants and identified thousands of large-effect variants (SNPs and indels) that occurred in about four hundred genes in hybs mutants. Seeds from both WT and hybs lines were sampled 20 days after flowering (DAF) and were used for RNA-Seq analysis; the results revealed about one thousand highly differentially expressed genes (DEGs) in hybs compared to WT. Using a method that combined large-effect variants with DEGs, we identified 45 potential candidate genes that shared gene product mutations and expression level changes in hybs compared to WT. Among the genes, two candidate genes encoding cytochrome P450 superfamily protein and NAC transcription factors may be associated with the increased seed size in hybs. The present findings provide new information on the identification and functional research into candidate genes responsible for the seed size phenotype in peanut.

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“…Twenty-two genes were predicted in this region, with two genes of interest, Aradu.RLZ61 and Aradu.DN3DB, encoding a transcriptional regulator, an F-box SNEEZY (SNE), and STERILE APETALA-like (SAP), respectively. These genes play a critical role in regulating seed and fruit size [ 67 ]. Moreover, MINI SEED 2 ( MIS2 ) regulates grain size by coordinately controlling epidermal cell number and cell size, and microscopic analysis showed that mis2 mutant rice revealed reduced cell size of spikelet epidermis but higher cell numbers [ 54 ].…”

Section: Genetic Factors Controlling Seed Sizementioning

confidence: 99%

Developing Genetic Engineering Techniques for Control of Seed Size and Yield

Alam

Batool

Huang

et al. 2022

IJMS

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Many signaling pathways regulate seed size through the development of endosperm and maternal tissues, which ultimately results in a range of variations in seed size or weight. Seed size can be determined through the development of zygotic tissues (endosperm and embryo) and maternal ovules. In addition, in some species such as rice, seed size is largely determined by husk growth. Transcription regulator factors are responsible for enhancing cell growth in the maternal ovule, resulting in seed growth. Phytohormones induce significant effects on entire features of growth and development of plants and also regulate seed size. Moreover, the vegetative parts are the major source of nutrients, including the majority of carbon and nitrogen-containing molecules for the reproductive part to control seed size. There is a need to increase the size of seeds without affecting the number of seeds in plants through conventional breeding programs to improve grain yield. In the past decades, many important genetic factors affecting seed size and yield have been identified and studied. These important factors constitute dynamic regulatory networks governing the seed size in response to environmental stimuli. In this review, we summarized recent advances regarding the molecular factors regulating seed size in Arabidopsis and other crops, followed by discussions on strategies to comprehend crops’ genetic and molecular aspects in balancing seed size and yield.

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Fine-Mapping of a Wild Genomic Region Involved in Pod and Seed Size Reduction on Chromosome A07 in Peanut (Arachis hypogaea L.)

Cited by 23 publications

References 65 publications

Transcriptome analysis of pod mutant reveals plant hormones are important regulators in controlling pod size in peanut (Arachis hypogaea L.)

Transcriptome analysis of pod mutant reveals plant hormones are important regulators in controlling pod size in peanut (Arachis hypogaea L.)

Multi-Omics Profiling Identifies Candidate Genes Controlling Seed Size in Peanut

Developing Genetic Engineering Techniques for Control of Seed Size and Yield

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