Principles and approaches of association mapping in plant breeding

Ibrahim, Aminu; Zhang, Lilan; Niyitanga, Sylvain; Afzal, Muhammad; Xu, Yi; Qi, Jianmin

doi:10.1007/s12042-020-09261-4

Cited by 47 publications

(41 citation statements)

References 99 publications

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“…Related to knowledge about combining ability, the extensive datasets for rootstock performance information of a large group of citrus hybrids can also be used to effectively map genes associated with important rootstock traits on the citrus genome. Molecular markers, association mapping, and quantitative trait locus mapping are common tools in plant breeding of annual crops, made practical by the use of test crosses and very short generation times ( Xu and Crouch, 2008 ; Ibrahim et al, 2020 ). Recent advances in data analysis demonstrate that similar mapping of genes can be accomplished from unbalanced and diverse multi-environment field trial data ( Rife et al, 2018 ; MacQueen et al, 2020 ), such as the data from the SuperSour strategy with 15 concurrent sweet orange rootstock trials and 350 hybrid rootstocks.…”

Section: Identify Superior Parental Combinations and Map Rootstock Traitsmentioning

confidence: 99%

SuperSour: A New Strategy for Breeding Superior Citrus Rootstocks

2021

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Citrus crops have a long history of cultivation as grafted trees on selected rootstock cultivars, but all current rootstocks have significant limitations and traditional methods of rootstock breeding take at least 2–3 decades to develop and field test new rootstocks. Citrus production in the United States, and other parts of the world, is impaired by a wide range of biotic and abiotic problems, with especially severe damage caused by the disease huanglongbing (HLB) associated with Candidatus Liberibacter asiaticus. All major commercial citrus scion cultivars are damaged by HLB, but tree tolerance is significantly improved by some rootstocks. To overcome these challenges, the USDA citrus breeding program has implemented a multi-pronged strategy for rootstock breeding that expands the diversity of germplasm utilized in rootstock breeding, significantly increases the number of new hybrids evaluated concurrently, and greatly reduces the time from cross to potential cultivar release. We describe the key components and methodologies of this new strategy, termed “SuperSour,” along with reference to the historical favorite rootstock sour orange (Citrus aurantium), and previous methods employed in citrus rootstock breeding. Rootstock propagation by cuttings and tissue culture is one key to the new strategy, and by avoiding the need for nucellar seeds, eliminates the 6- to 15-year delay in testing while waiting for new hybrids to fruit. In addition, avoiding selection of parents and progeny based on nucellar polyembryony vastly expands the potential genepool for use in rootstock improvement. Fifteen new field trials with more than 350 new hybrid rootstocks have been established under the SuperSour strategy in the last 8 years. Detailed multi-year performance data from the trials will be used to identify superior rootstocks for commercial release, and to map important traits and develop molecular markers for the next generation of rootstock development. Results from two of these multi-year replicated field trials with sweet orange scion are presented to illustrate performance of 97 new hybrid rootstocks relative to four commercial rootstocks. Through the first 7 years in the field with endemic HLB, many of the new SuperSour hybrid rootstocks exhibit greatly superior fruit yield, yield efficiency, canopy health, and fruit quality, as compared with the standard rootstocks included in the trials.

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Section: Identify Superior Parental Combinations and Map Rootstock Traitsmentioning

confidence: 99%

SuperSour: A New Strategy for Breeding Superior Citrus Rootstocks

2021

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“…Pada deteksi hubungan marka dan fenotipe dalam kajian association mapping, pemilihan contoh plasma nutfah merupakan hal yang penting, selain mutu data genotipe dan fenotipe, pemilihan analisis statistika yang sesuai, serta verifikasi asosiasinya (Ibrahim et al, 2020). Pada kajian ini, contoh yang dipilih terdiri dari tetua E. oleifera tipe liar dari Suriname dan Brazil, individu E. guineensis maju, dan berbagai hasil persilangan meliputi F1 hibrida interspesifik dan pseudo-backcross (Tabel 1).…”

Section: Hasil Dan Pembahasan Seleksi Genotipe Dan Pengurutanunclassified

Identifikasi SNP genom pada populasi Elaeis guineensis x Elaeis oleifera

Wening

Siregar

Suprianto

et al. 2021

J. Penelitian Kelapa Sawit

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Usaha pencarian marka DNA yang berhubungan dengan sifat yang diinginkan pada Elaeis oleifera guna introgresi sifat tersebut ke genome Elaeis guineensis memerlukan marka DNA yang polimorfik. Untuk menghasilkan marka DNA yang polimorfik dengan jumlah banyak, identifikasi SNP genom dilakukan melalui pengurutan kembali (resequencing) 12 individu contoh populasi hibrida E. guineensis x E. oleifera (hibrida OxG), yaitu E. oleifera tipe liar, F1 hibrida interspesifik, pseudo-backcross dan material maju E. guineensis, menggunakan next generation sequencing (NGS). Read (urutan basa yang “dibaca”/merupakan keluaran mesin NGS) dari 12 contoh memiliki mutu yang baik dan 96% total read yang disaring dapat dilakukan demultipleks dan ditentukan pada contoh yang sesuai. Setelah proses penyaringan dan pemotongan, 84% read dapat digunakan untuk pemetaan genom dan menghasilkan 5,7X hingga 10,42X cakupan genom. Dari 34.410.224 SNP yang teridentifikasi, 98,7% diantaranya adalah varian non-coding, dan berdasarkan lokasi, 69,1% total SNP adalah SNP intergenic. Sebanyak 5.618 SNP dari total SNP yang dihasilkan dibuktikan menggunakan targeted genotyping by sequencing pada 500 individu contoh. Sebanyak 74% SNP yang digunakan bermutu tinggi yang dibaca pada setidaknya 95% contoh. Principal component analysis menggunakan SNP tersebut mampu mengidentifikasi setiap latar belakang genetik contoh. Pembuktian tersebut menyimpulkan bahwa identifikasi SNP yang dilakukan melalui pengurutan kembali menghasilkan SNP bermutu tinggi yang dapat digunakan untuk pengembangan marka DNA yang dapat diperbantukan pada seleksi populasi pemuliaan E. guineensis x E. oleifera.

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“…Finding the genetic loci regulating the FT-tolerant trait is crucial for developing FT-tolerant rice accessions. Association mapping utilized historical recombination and mutation events within a population to accurately detect marker-trait association [54]. Nevertheless, association mapping can suffer from false-positive results due to population structure and family relatedness [55].…”

Section: Discussionmentioning

confidence: 99%

Genome-Wide Association Study of Local Thai Indica Rice Seedlings Exposed to Excessive Iron

Kaewcheenchai

Vejchasarn²,

Hanada

et al. 2021

Plants

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Excess soluble iron in acidic soil is an unfavorable environment that can reduce rice production. To better understand the tolerance mechanism and identify genetic loci associated with iron toxicity (FT) tolerance in a highly diverse indica Thai rice population, a genome-wide association study (GWAS) was performed using genotyping by sequencing and six phenotypic data (leaf bronzing score (LBS), chlorophyll content, shoot height, root length, shoot biomass, and root dry weight) under both normal and FT conditions. LBS showed a high negative correlation with the ratio of chlorophyll content and shoot biomass, indicating the FT-tolerant accessions can regulate cellular homeostasis when encountering stress. Sixteen significant single nucleotide polymorphisms (SNPs) were identified by association mapping. Validation of candidate SNP using other FT-tolerant accessions revealed that SNP:2_21262165 might be associated with tolerance to FT; therefore, it could be used for SNP marker development. Among the candidate genes controlling FT tolerance, RAR1 encodes an innate immune responsive protein that links to cellular redox homeostasis via interacting with abiotic stress-responsive Hsp90. Future research may apply the knowledge obtained from this study in the molecular breeding program to develop FT-tolerant rice varieties.

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Principles and approaches of association mapping in plant breeding

Cited by 47 publications

References 99 publications

SuperSour: A New Strategy for Breeding Superior Citrus Rootstocks

SuperSour: A New Strategy for Breeding Superior Citrus Rootstocks

Identifikasi SNP genom pada populasi Elaeis guineensis x Elaeis oleifera

Genome-Wide Association Study of Local Thai Indica Rice Seedlings Exposed to Excessive Iron

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