Phenotyping and genotyping parents of sixteen recombinant inbred peanut populations

Chu, Ye; Holbrook, C. Corley; Isleib, T. G.; Burow, Mark D.; Culbreath, A. K.; Tillman, Barry L.; Chen, Jing; Clevenger, Josh; Ozias‐Akins, Peggy

doi:10.3146/ps17-17.1

Cited by 13 publications

(14 citation statements)

References 52 publications

(44 reference statements)

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“…Similarly, the USDA-ARS and the University of Georgia (UGA) developed two NAM populations, namely 'NAM_Florida' and 'NAM_Tifrunner,' using Florida-07 and Tifrunner as common parents and crossing with four founder parental genotypes (N08082, SPT06-06, C76-16 and NC3033). These NAM populations segregate for several agronomic traits in addition to resistance to tomato spotted wilt virus (TSWV), aflatoxin resistance, drought tolerance, early and late leaf spot resistance (Holbrook et al 2013;Chu et al 2018. In USA, a MAGIC population was also developed from eight founders: SunOleic 97R, NC94022, Tifrunner, GT-C20, Florida 07, SPT06-06, Georgia 13 M and TifNV-High O/L.…”

Section: Genetic Resources For High-resolution Mappingmentioning

confidence: 99%

Translational genomics for achieving higher genetic gains in groundnut

Pandey

Kumar

et al. 2020

Theor Appl Genet

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Key message Groundnut has entered now in post-genome era enriched with optimum genomic and genetic resources to facilitate faster trait dissection, gene discovery and accelerated genetic improvement for developing climate-smart varieties. Abstract Cultivated groundnut or peanut (Arachis hypogaea), an allopolyploid oilseed crop with a large and complex genome, is one of the most nutritious food. This crop is grown in more than 100 countries, and the low productivity has remained the biggest challenge in the semiarid tropics. Recently, the groundnut research community has witnessed fast progress and achieved several key milestones in genomics research including genome sequence assemblies of wild diploid progenitors, wild tetraploid and both the subspecies of cultivated tetraploids, resequencing of diverse germplasm lines, genome-wide transcriptome atlas and cost-effective high and low-density genotyping assays. These genomic resources have enabled high-resolution trait mapping by using germplasm diversity panels and multi-parent genetic populations leading to precise gene discovery and diagnostic marker development. Furthermore, development and deployment of diagnostic markers have facilitated screening early generation populations as well as marker-assisted backcrossing breeding leading to development and commercialization of some molecular breeding products in groundnut. Several new genomics applications/technologies such as genomic selection, speed breeding, mid-density genotyping assay and genome editing are in pipeline. The integration of these new technologies hold great promise for developing climate-smart, high yielding and more nutritious groundnut varieties in the post-genome era.

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Section: Genetic Resources For High-resolution Mappingmentioning

confidence: 99%

Translational genomics for achieving higher genetic gains in groundnut

Pandey

Kumar

et al. 2020

Theor Appl Genet

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“…While the array was designed to have broad application in Arachis genome analysis, it is especially useful for genotyping A. hypogaea × A. hypogaea populations. The array includes 21,547 and 22,933 markers targeting the A and B genomes, respectively, selected based on a panel of A. hypogaea genotypes which includes parents of RIL populations segregating for resistance to multiple diseases, abiotic stress tolerance, pod and seed characteristics, and yield (Chu et al 2018;Clevenger et al 2017;Holbrook et al 2013). In this study, this new array technology was utilized to genotype a recombinant inbred population to develop a SNPbased linkage map and detect QTL for pod and seed size traits.…”

Section: Introductionmentioning

confidence: 99%

Major seed size QTL on chromosome A05 of peanut (Arachis hypogaea) is conserved in the US mini core germplasm collection

et al. 2019

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Pod and seed size are important characteristics for the peanut industry and have been under strong selection pressure since peanut domestication. In order to dissect the genetic control of peanut pod and seed size, a recombinant inbred mapping population from a cross of Florida-07 by GP-NC WS 16 was used to determine the genomic regions associated with traits including 100 pod weight, 100 seed weight, pod weight of double-seeded pods, seed weight of double-seeded pods, and area of double-seeded pods. Nine QTL on linkage groups (LGs) A05, A06, A09, B10, B04, A03, B05, and B08 were associated with pod and seed size. A majority of the QTL have small effects except the locus on LG A05 (93 to 102 Mbp) which explained up to 66% phenotypic variation for all measured pod and seed traits. A comparison of QTL previously reported for yield component traits showed a common QTL on LG A05 was detected in two genetic populations whose parentage is distinct from those used in this study. The markers tightly linked to this major QTL were informative in distinguishing large versus small-seeded germplasm lines in the mini core collection originating from thirty-one countries, suggesting selection for this seed size QTL in large-seeded ecotypes. However, the large seed size allele appeared to co-segregate with a late leaf spot disease susceptibility allele inherited from the Florida-07 parent. Therefore, peanut breeders need to weigh the pros and cons before integrating the large seed size QTL from Florida-07 in their breeding program.

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“…Recently, assemblies of reference genome have also become available for cultivated peanut (Bertioli et al , ; Chen et al , ; Zhuang et al , ) and will increase the efficiency of such studies in the future. In this study, we have used two NAM populations of set A (Chu et al , ; Holbrook et al , ) and a highly informative ‘Axiom_ Arachis ’ SNP array which was based on two peanut progenitor genome sequences (Chavarro et al , ; Clevenger et al , ; Pandey et al , ) for genotyping both NAM populations.…”

Section: Discussionmentioning

confidence: 99%

“…Two NAM populations namely ‘NAM_Tifrunner’ (NAM‐T) and ‘NAM_Florida‐07’ (NAM‐F) were defined by using a subset of the Set A (which was only available at that time) RIL populations developed by peanut research community (Chu et al , ; Holbrook et al , ), two runner cultivars (Tifrunner and Florida‐07) as common parents and four unique parents of N08082olJCT, C76‐16, NC 3033 and GP‐NC WS16 (SPT 06‐06) (Tallury et al , ). NAM‐T had 581 RILs and NAM‐F had 496 RILs.…”

Section: Methodsmentioning

confidence: 99%

“…Several years ago, U.S. peanut research community developed two NAM mapping populations with two common parents (Tifrunner and Florida‐07) and eight diverse, unique parents, resulting in 16 biparental recombinant inbred line (RIL) families in order to maximize genetic diversity while meeting practical breeding objectives (Holbrook et al , ). The primary objective of this developed genetic resource was to share these populations with the peanut research community and to undertake high‐resolution phenotyping of these populations (Chu et al , ; Holbrook et al , ). The parents represent a wide range of agronomic, morphological and disease resistance traits, and some biparental populations have been studied for resistance to early and late leaf spot diseases (Chu et al , ; Clevenger et al , ).…”

Section: Introductionmentioning

confidence: 99%

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Nested‐association mapping (NAM)‐based genetic dissection uncovers candidate genes for seed and pod weights in peanut (Arachis hypogaea)

Gangurde

Wang

Shasidhar

et al. 2019

Plant Biotechnology Journal

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email baozhu.guo@usda.gov (B. G.); Tel 91-40-30713345; fax 91-40-30713074; email r.k.varshney@cgiar.org (R. K. V.)) † These authors contributed equally to this study. SummaryMultiparental genetic mapping populations such as nested-association mapping (NAM) have great potential for investigating quantitative traits and associated genomic regions leading to rapid discovery of candidate genes and markers. To demonstrate the utility and power of this approach, two NAM populations, NAM_Tifrunner and NAM_Florida-07, were used for dissecting genetic control of 100-pod weight (PW) and 100-seed weight (SW) in peanut. Two high-density SNP-based genetic maps were constructed with 3341 loci and 2668 loci for NAM_Tifrunner and NAM_Florida-07, respectively. The quantitative trait locus (QTL) analysis identified 12 and 8 major effect QTLs for PW and SW, respectively, in NAM_Tifrunner, and 13 and 11 major effect QTLs for PW and SW, respectively, in NAM_Florida-07. Most of the QTLs associated with PW and SW were mapped on the chromosomes A05, A06, B05 and B06. A genomewide association study (GWAS) analysis identified 19 and 28 highly significant SNP-trait associations (STAs) in NAM_Tifrunner and 11 and 17 STAs in NAM_Florida-07 for PW and SW, respectively. These significant STAs were co-localized, suggesting that PW and SW are co-regulated by several candidate genes identified on chromosomes A05, A06, B05, and B06. This study demonstrates the utility of NAM population for genetic dissection of complex traits and performing highresolution trait mapping in peanut.

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Phenotyping and genotyping parents of sixteen recombinant inbred peanut populations

Cited by 13 publications

References 52 publications

Translational genomics for achieving higher genetic gains in groundnut

Translational genomics for achieving higher genetic gains in groundnut

Major seed size QTL on chromosome A05 of peanut (Arachis hypogaea) is conserved in the US mini core germplasm collection

Nested‐association mapping (NAM)‐based genetic dissection uncovers candidate genes for seed and pod weights in peanut (Arachis hypogaea)

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