Breeding History Research Articles

Single-Step Breeding Value Estimations and Optimum Contribution Selection in Endangered Dual-Purpose German Black Pied Cattle (DSN) Using a Breed Specific SNP Chip.

The aims of the present study were to perform single-step genomic predictions in the dual-purpose German Black Pied cattle (DSN) breed considering a DSN specific SNP chip (DSN_200 K), and to use the corresponding estimated breeding values (EBV) in ongoing optimum genetic contribution (OGC) selection. All results were compared with the application of the commercial Illumina BovineSNP50 BeadChip (50 K). The traits of interest in the present study (due to the differing breeding history of these traits in the past) included 305-day lactation protein percentage (Pro%) of 9029 DSN cows, fat-to-protein ratio (FPR) from the first test-day of 8773 DSN cows, and stature (STAT) measured in cm of 4409 DSN cows. The DSN cows represented the calving years 2008-2019. Genotyping of 2797 DSN animals was conducted using both the DSN_200 K and the 50 K. From the genotyped animals, a subset of 1800 cows had phenotypic records for all three traits FPR, Pro% and STAT. Heritabilities from the single-step genetic parameter estimations were quite large for Pro% (0.69) and STAT (0.78), but small for FPR (0.11). The choice of the SNP chip only had minor effects on variance components, heritabilities and EBVs. Furthermore, genetic parameters were very similar from genetic-statistical models additionally considering a linear regression on pedigree-based inbreeding coefficients. OGC selection was applied to a pool of 1125 pre-selected bull sires (BS) and bull dams (BD). A more relaxed genetic relationship constraint was associated with favourable effects on the average EBVs for Pro%, FPR and STAT, and a declining number of selected BS. The gains in genetic merit were marginal when relaxing the constraint at 0.06 for the genetic relationships or higher. The same associations were found for an overall breeding index (I-DSN), considering the three traits with equal weights. Consequently, we suggested OGC applications with a genetic relationship constraint of 0.06, which contributed to genetic gain in I-DSN of 17.9%, and to increased diversity due to an increased number of BS, when compared to the current practical elite animal selection scheme. A large number of finally selected BS and BD was identical when either using EBV from the DSN_200 K or from the 50 K. From such perspective, we only see marginal extra value for the specific DSN SNP-chip application.

Peritoneal dialysis-associated peritonitis caused by Coxiella Burnetii: A case report.

Peritoneal dialysis (PD)-associated peritonitis (PDAP) is the leading cause of PD failure and discontinuation of PD. Several zoonotic pathogens could lead to the development of PDAP. Coxiella burnetii (C. burnetii) was a zoonotic pathogen and the cause of Q fever. However, reports of PDAP caused by C. burnetii are rare. We herein report the first case of PDAP caused by C. burnetii in mainland China. A 45-year-old woman was admitted to our hospital with chief complaint of yellow and cloudy PD effluent for 2 days. She had undergone PD for 5 years due to end-stage renal disease. She was engaged in cattle and sheep breeding. The culture of PD effluent was negative, even for specific species, such as Mycobacteria and fungi. The culture from the PD effluent tested positive for C. burnetii by adopting metagenomic next-generation sequencing on day 37. We diagnosed her as PDAP caused by C. burnetii. Empirical treatment with multiple broad-spectrum antibiotics (including vancomycin, etimicin, piperacillin) was initially adopted. After identifying C. burnetii as the culprint as the PDAP, the regimen was changed to doxycycline (100 mg twice daily) and moxifloxacin (400 mg once daily) orally, leading to clinical improvement. The white blood cell count of the PD effluent decreased to within the normal range and the culture of PD effluent was negative for C. burnetii at the visit of 4 months after discharge. Also, there was no sign for recurrence. Vigilance should be heightened for PDAP cases with negative culture of PD fluid and poor response to standard broad-spectrum antibiotic treatment, along with a history of cattle and sheep breeding. In such conditions, PD effluent should be tested to detect possible peritonitis caused by C. burnetii, even in patients without symptoms of fever. Prompt pathogen identification and appropriate treatment are crucial for clinical improvement of such cases.

The Gut Bacteria of Gampsocleis gratiosa (Orthoptera: Tettigoniidae) by Culturomics

Gampsocleis gratiosa Brunner von Wattenwyl, 1862, is a type of omnivorous chirping insect with a long history of artificial breeding. It has high economic value and is also an excellent orthopteran model organism. In this study, 12 types of culture media combined with 16S rRNA sequencing were employed to isolate 838 bacterial strains from the gut of G. gratiosa. After sequence comparison, a total of 98 species of bacteria were identified, belonging to 3 phyla, 5 classes, 11 orders, 20 families, and 45 genera. Firmicutes and Proteobacteria accounted for the majority (92.86%). At the order level, Enterobacteriaceae, Bacillales, and Lactobacillales predominated (79.59%). At the genus level, Klebsiella (11.22%) and Enterococcus (7.14%) predominated. This study also enumerated the strain morphological, physiological and biochemical properties of 98 species of bacteria, including colony morphology, Gram staining, bacterial motility test, temperature gradient growth, pH gradient growth, citrate utilization test, temperature oxidase test, contact enzyme test, methyl red test, V-P test, indole test, gelatin liquefaction test, nitrate reduction test, hydrogen sulfide test, starch hydrolysis test, cellulose decomposition test, esterase (corn oil) test and antibiotic susceptibility testing. Additionally, 16 antibiotics were utilized to test the bacterial susceptibility of the strains. This study explored the types and community structure of some culturable microorganisms in the intestinal tract of G. gratiosa and recorded their physiological characteristics. These data reflect the physiological functions of the intestinal microorganisms of G. gratiosa and provide support for subsequent research on the interaction mechanism between microorganisms and their hosts.

Pseudopregnancy in dromedary camels: Characterization, prevalence, and clinical and hormonal properties.

Pseudopregnancy is the development of signs of pregnancy in the absence of an embryo or fetus. The objectives of this study were to characterize pseudopregnancy in dromedary camels, determine its prevalence in camel farms and practice, identify associated risk factors, and describe its clinical and hormonal properties. The prevalence of pseudopregnancy on 100 camel farms with 4264 total female camels was determined to be 2.07% (86/4264) overall, while the rate among infertile animals was 17.68% (1385/7833). The genital tracts of 58 pseudopregnant female camels were examined, and their breeding histories were examined. Serum concentrations of estradiol-17 β (E2), progesterone (P4), and prolactin (PRL) in these animals were assessed. Five cyclic camels and five in early pregnancy were used as control subjects. Signs of pseudopregnancy included being anestrous, refusing to mate, and adopting a stiffened posture-with the head held high and the tail cocked-when approached by a male. Normal pregnancy-associated mammary and abdominal changes were absent. Risk factors associated with pseudopregnancy included age (odds ratio [OR]=21.63, P=0.0001) and a history of reproductive disorders (OR=4.155, P=0.042). Based on their P4 levels, the pseudopregnant camels were classified as either typical (high P4, 16/58, 27.59%) or atypical (low P4, 42/58, 72.41%). The main clinical findings in the camels with typical pseudopregnancies were a narrow/closed cervix (56.25%), clinical endometritis (CE; 43.75%), and pyometra (31.25%), while those with atypical pseudopregnancies exhibited CE (50%) and luteinized follicles (43.1%). The pregnant camels had significantly (P=0.0001) higher serum P4 concentrations (2.44±0.32ng/mL) than the pseudopregnant (0.68±0.12ng/mL) and cyclic camels (0.16±0.01ng/mL). Serum E2 levels did not differ significantly among the pseudopregnant (43.2±1.05pg/mL), pregnant (47.72±4.06pg/mL), and cyclic (40.72±1.03pg/mL) camels. The pregnant camels had a significantly (P=0.04) higher average serum PRL concentration (3.61±0.45ng/mL) than the pseudopregnant (2.77±0.12ng/mL) and cyclic camels (2.18±0.11). In conclusion, pseudopregnancy in camels exhibits the same external signs that characterize pregnancy, but pseudopregnancy involves an absence of edema of the udder, milk production, and high PRL levels. We propose a division of pseudopregnant camels into typical and atypical classes, depending on whether they have high P4 levels. Pseudopregnancy is associated with a high incidence of other reproductive disorders, particularly in older camels.

The highly allo-autopolyploid modern sugarcane genome and very recent allopolyploidization in Saccharum.

Modern sugarcane, a highly allo-autopolyploid organism, has a very complex genome. In the present study, the karyotype and genome architecture of modern sugarcane were investigated, resulting in a genome assembly of 97 chromosomes (8.84 Gb). The allopolyploid genome was divided into subgenomes from Saccharum officinarum (Soh) and S. spontaneum (Ssh), with Soh dominance in the Saccharum hybrid (S. hybrid). Genome shock affected transcriptome dynamics during allopolyploidization. Analysis of an inbreeding population with 192 individuals revealed the underlying genetic basis of transgressive segregation. Population genomics of 310 Saccharum accessions clarified the breeding history of modern sugarcane. Using the haplotype-resolved S. hybrid genome as a reference, genome-wide association studies identified a potential candidate gene for sugar content from S. spontaneum. These findings illuminate the complex genome evolution of allopolyploids, offering opportunities for genomic enhancements and innovative breeding strategies for sugarcane.

Genome of root celery and population genomic analysis reveal the complex breeding history of celery.

Celery (Apium graveolens L.) is an important vegetable crop in the Apiaceae family. It comprises three botanical varieties: common celery with solid and succulent petioles, celeriac or root celery with enlarged and fleshy hypocotyls and smallage or leaf celery with slender, leafy and usually hollow petioles. Here we present a chromosome-level genome assembly of a celeriac cultivar and a comprehensive genome variation map constructed through resequencing of 177 representative celery accessions. Phylogenetic analysis revealed that smallage from the Mediterranean region represented the most ancient type of cultivated celery. Following initial domestication in this region, artificial selection has primarily aimed at enlarging the hypocotyl, resulting in celeriac, and at solidifying the petiole, leading to common celery. Selective sweep analysis and genome-wide association study identified several genes associated with hypocotyl expansion and revealed that the hollow/solid petiole trait directly correlated with the presence/absence of a NAC gene. Our study elucidates the complex breeding history of celery and provides valuable genomic resources and molecular insights for future celery improvement and conservation efforts.

Refining polyploid breeding in sweet potato through allele dosage enhancement.

Allele dosage plays a key role in the phenotypic variation of polyploids. Here we present a genome-wide variation map of hexaploid sweet potato that captures allele dosage information, constructed from deep sequencing of 294 hexaploid accessions. Genome-wide association studies identified quantitative trait loci with dosage effects on 23 agronomic traits. Our analyses reveal that sweet potato breeding has progressively increased the dosage of favourable alleles to enhance trait performance. Notably, the Mesoamerican gene pool has evolved towards higher dosages of favourable alleles at multiple loci, which have been increasingly introgressed into modern Chinese cultivars. We substantiated the breeding-driven dosage accumulation through transgenic validation of IbEXPA4, an expansin gene influencing tuberous root weight. In addition, we explored causative sequence variations that alter the expression of the Orange gene, which regulates flesh colour. Our findings illuminate the breeding history of sweet potato and establish a foundation for leveraging allele dosages in polyploid breeding practices.

Functional nutritional rice: current progresses and future prospects.

More than half of the world's population relies on rice as their staple food for three meals a day. From a dietary perspective, rice can be considered the most important grain in the world. With the continuous improvement of people's living standards, the demand for food has gradually shifted from being full and eating well to being nutritious and healthy. Developing functional nutritional rice has become an important research direction and strategic initiative for developing a major food concept. In this paper, we review the current progress in the breeding of functional nutritional rice and mineral-biofortified rice. This review focuses on the following aspects: (i) the concept, rice basic structure, nutritional components, and categorization of functional nutritional rice; (ii) genes that have been applied and identified so far, including nutritional functional rice genes, mineral bioenhancement-related genes, and their regulatory mechanisms; (iii) based on the history and technical mainline of rice breeding, research progress in nutritional functional rice using conventional breeding, a combination of conventional breeding and marker-assisted breeding, mutagenesis breeding, genetic engineering technology, and gene editing technology. Based on the current research and industrialization issues, we highlight an outlook of the problems and future developmental directions in nutritional functional rice research.

The global spread of Oriental Horses in the past 1,500 years through the lens of the Y chromosome

Since their domestication, horses have accompanied mankind, and humans have constantly shaped horses according to their needs through stallion-centered breeding. Consequently, the male-specific portion of the Y chromosome (MSY) is extremely uniform in modern horse breeds. The majority of stallions worldwide carry MSY haplotypes (HT) attributed to an only ~1,500-y-old, so-called, "Crown" haplogroup. The predominance of the Crown in modern horse breeds is thought to represent a footprint of the vast impact of stallions of "Oriental origin" in the past millennium. Here, we report the results of a fine-scaled MSY haplotyping of large datasets of patrilines comprising 1,517 males of 189 modern horse breeds, covering a broad phenotypic and geographic spectrum. We can disentangle the multilayered influence of Oriental stallions over the last few hundred years, exposing the intense linebreeding and the wide-ranging impact of Arabian, English Thoroughbred, and Coldblood sires. Iberian and New World horse breeds contain a wide range of diversified Crown lineages. Their broad HT spectrum illustrates the spread of horses of Oriental origin via the Iberian Peninsula after the Middle Ages, which is commonly referred to as the "Spanish influence." Our survey also revealed a second major historical dissemination of horses from Western Asia, attributed to the expansion of the Ottoman Empire. Our analysis shows that MSY analysis can uncover the complex history of horse breeds and can be used to establish the paternal ancestry of modern horse breeds.

A metabolic roadmap of waxy corn flavor

As well as being a popular vegetable crop worldwide, waxy corn represents an important amylopectin source, but little is known about its breeding history and flavor characteristics. In this study, through comparative-omic analyses between 318 diverse waxy corn and 507 representative field corn inbred lines we revealed that many metabolic pathways and genes exhibited selection characteristics during the breeding history of waxy corn, contributing to the divergence between waxy and field corn. We showed that waxy corn is not only altered in its glutinous property but also its sweetness, aroma, and palatability are all significantly affected. A substantial proportion (43%) of flavor-related metabolites have pleiotropic effects, affecting both flavor and yield characteristics, and 27% of these metabolites are related to antagonistic outcomes on yield and flavor. Furthermore, through multiple concrete examples, we demonstrated how yield and quality are coordinately or antagonistically regulated at the genetic level. In particular, some sweet molecules, such as DIMBOA and raffinose, which do not participate in the starch biosynthesis pathway, were identified as potential targets for breeding a new type of “sweet-waxy” corn. Taken together, our findings shed light on the historical selection of waxy corn and demonstrate the genetic and metabolic basis of waxy corn flavor, collectively providing valuable resources and knowledge for future crop breeding for improved nutritional quality.

The history of the breeding of Clematis (Clematis L.) in the M. M. Gryshko National Botanical Garden, NAS of Ukraine

Purpose. Investigate the history of Clematis breeding in the M. M. Gryshko National Botanical Garden (NBG), NAS of Ukraine, determine the main directions of hybrid Clematis breeding work. Results. It was established that the result of more than 16 years of breeding Clematis in the NBG was the selection of the 61 perspective hybrid, 42 of which, the most perspective, were assigned names. Of these, large­flowered varieties are the most numerous according to the distribution of variety groups in the current Royal Horticultural Society of Great Britain classification. In particular, Late Large­flowered account for about 40% of the total and Early Large­flowered for about 29%. Small­flowered hybrids make up the smaller part, of which about 26% belong to the Viticella group and one hybrid (‘Sputnik’) to the Integrifolia. The known directions of distribution of hybrid Сlematis of the NBG breeding indicate the possibility of their successful cultivation both in continental and maritime areas with a high level of humidity in the temperate zone and in the dry Mediterranean climate of the subtropical climate zone, which reveals their significant adaptive potential. Conclusions. Obtaining varieties of hybrid Clematis of domestic breeding is important for the implementation of sustainable horticulture practices on the territory of Ukraine, since a significant part of the modern introduced assortment of Clematis raises doubts about their adaptability to the local climate, and requires additional research into their adaptive potential. A successful combination in vertical landscaping of NBG­bred Clematis belonging to different varietal groups can ensure continuous flowering from May to the end of the season. These unique characteristics of Clematis ensure the creation of not only environmentally sustainable, but also visually appealing spaces that will contribute to the overall health and beauty of the urban environment.

Chloroplast genome sequencing and divergence analysis of 18 Pyrus species: insights into intron length polymorphisms and evolutionary processes.

Pears constitute an essential temperate crop and are primarily produced through interspecific hybridization owing to self-incompatibility that complicates their breeding history. To address this, we sequenced the complete chloroplast (cp) genomes of 18 Pyrus and one Malus species using the Illumina HiSeq4000 platform. The cp genomes ranged from 159,885 bp to 160,153bp and exhibited a conserved circular DNA structure with an average GC content of 36.5%. Each cp genome contained 127 genes, including 83 protein-coding, 36 tRNA, and 8 rRNA genes. Divergence analysis with mVISTA showed high conservation in the coding regions and notable variations in the non-coding regions. All species shared 17 intron-containing genes, with ycf3 and clpP each having two introns. Five intron-containing genes (ndhB, rpl2, rps12, trnA-UGC, and trnE-UUC) were located in the inverted repeat regions, while trnL-UAA was located in the large single-copy region, with conserved intron lengths across Pomoideae. We identified polymorphic intron sequences in the rpl22, petB, clpP, ndhA, and rps16 genes and designed primers for these regions. Notably, the two Pyrus ussuriensis accessions Doonggeullebae and Cheongdangrori showed intron-length polymorphisms despite being classified as the same species. Phylogenetic analysis of the cp genome sequences revealed two major clusters, indicating distinct maternal lineages and evolutionary origins. This study underscores the importance of cp gene polymorphisms in P. fauriei, P. calleryana, P. ussuriensis, and P. pyrifolia, providing valuable insights into Pyrus evolution as well as aiding in the conservation and breeding of pear germplasm.

Unravelling the complex origin and breeding history of modern roses.

Unravelling the complex origin and breeding history of modern roses.

Haplotype-resolved genome assembly and resequencing provide insights into the origin and breeding of modern rose.

Modern rose (Rosa hybrida) is a recently formed interspecific hybrid and has become one of the most important and widely cultivated ornamentals. Here we report the haplotype-resolved chromosome-scale genome assembly of the tetraploid R. hybrida 'Samantha' ('JACmantha') and a genome variation map of 233 Rosa accessions involving various wild species, and old and modern cultivars. Homologous chromosomes of 'Samantha' exhibit frequent homoeologous exchanges. Population genomic and genomic composition analyses reveal the contributions of wild Rosa species to modern roses and highlight that R. odorata and its derived cultivars are important contributors to modern roses, much like R. chinensis 'Old Blush'. Furthermore, selective sweeps during modern rose breeding associated with major agronomic traits, including continuous and recurrent flowering, double flower, flower senescence and disease resistance, are identified. This study provides insights into the genetic basis of modern rose origin and breeding history, and offers unprecedented genomic resources for rose improvement.

The goat pan-genome reveals patterns of gene loss during domestication

BackgroundUnveiling genetic diversity features and understanding the genetic mechanisms of diverse goat phenotypes are pivotal in facilitating the preservation and utilization of these genetic resources. However, the total genetic diversity within a species can’t be captured by the reference genome of a single individual. The pan-genome is a collection of all the DNA sequences that occur in a species, and it is expected to capture the total genomic diversity of the specific species.ResultsWe constructed a goat pan-genome using map-to-pan assemble based on 813 individuals, including 723 domestic goats and 90 samples from their wild relatives, which presented a broad regional and global representation. In total, 146 Mb sequences and 974 genes were identified as absent from the reference genome (ARS1.2; GCF_001704415.2). We identified 3,190 novel single nucleotide polymorphisms (SNPs) using the pan-genome analysis. These novel SNPs could properly reveal the population structure of domestic goats and their wild relatives. Presence/absence variation (PAV) analysis revealed gene loss and intense negative selection during domestication and improvement.ConclusionsOur research highlights the importance of the goat pan-genome in capturing the missing genetic variations. It reveals the changes in genomic architecture during goat domestication and improvement, such as gene loss. This improves our understanding of the evolutionary and breeding history of goats.

Revolutionizing plant breeding: a historical perspective from cross-pollination to gene editing

The history of plant breeding can be broadly divided into four eras: the Pre-Mendelian era (before 1900), the Mendelian era (1900-1920), the post-Mendelian era (1921-1950), and the Modern era (after 1950). Significant milestones include the release of the first hybrid maize varieties in 1961, the first sorghum hybrid (CSH-1) in 1964, the first bajra hybrid (HB-1) in 1965, and the first pigeon pea hybrid (ICPH-8) in 1991. Achieving a world with zero hunger requires a sustainable increase in food production and distribution and elimination of poverty. This goal demands scientific, logistical, and humanitarian approaches to ensure food security from farmers and breeders to policymakers and governments. Conventional breeding techniques alone are insufficient to meet the challenges posed by climate change, biotic and abiotic stress, and the growing global population projected to reach 10 billion by 2050. Novel plant breeding techniques, such as genome editing, speed breeding, and omics technology integration, offer precise, cost-effective, and less time-consuming solutions. These techniques enable the editing of agriculturally significant genes, promoting hybrid seed production, induced apomixis, and resistance to biotic and abiotic stress. Genome editing technologies have evolved, with CRISPR/Cas9 and its variants, base editing (BE), and prime editing (PE) playing pivotal roles in generating transgene-free plants. These advancements have significant implications for crop improvement, meeting food and nutrition security, and catering to regional preferences. Syngenta's initiative to open rights to CRISPR-based technologies through the Shoots by Syngenta platform exemplifies the collaborative efforts needed to drive agricultural innovation and sustainability. The review discusses the current regulatory regimes governing genome-edited crops, prospects of new tools such as DNA-free editing systems and nanotechnology, and their applicability in crop improvement. A multidisciplinary approach involving political, social, economic, and scientific stakeholders is essential for the successful adoption of genome editing technologies, which will ultimately make agriculture a lucrative profession and attract youth to the field.

SAAZ—Fine Aroma Hop Pedigree: A Review of Current Knowledge

The hop variety Saaz is well known over the world and is usually used for brewing of lager beers. Recently, the new related varieties Saaz Late, Brilliant, Comfort, and Shine were registered. Information about these varieties is splintered and often available only in the Czech language in regional journals. This review (i) summarizes previously published data (breeding history, genetic data, basic parameters such as yield, sensory profile, concentrations of key technologically important hop compounds), (ii) presents long-term data (2004–2021), and (iii) shows similarities/differences among these varieties. All Saaz varieties are typically fine aroma hops with a relatively low content of alpha bitter acids ranging from 5 to 7 wt%, cohumulone amounts lower than 30% rel., and hop oil content of about 1.0 wt%. Even though the new varieties have no identical chemical parameters to the original Saaz, they can substitute this established standard as well. Furthermore, the varieties Saaz Comfort and Saaz Shine show high resistance to Pseudoperonospora humuli as well as very good tolerance to drought.

Whole-genome resequencing reveals melanin deposition candidate genes of Luning chicken

BackgroundMelanin in the black-bone chicken’s body is considered the material basis for its medicinal effects and is an economically important trait. Therefore, improving the melanin content is a crucial focus in the breeding process of black-bone chickens. Luning chickens are black-bone chickens, with black beaks, skin, and meat. To investigate the genetic diversity and molecular mechanisms of melanin deposition in Luning chickens, we conducted whole-genome resequencing to analyze their breeding history and identify candidate genes influencing their black phenotype, along with transcriptome sequencing of dorsal skin tissues of male Luning chickens.ResultsPopulation structure analysis revealed that Luning chickens tend to cluster independently and are closely related to Tibetan chickens. Runs of homozygosity analysis suggested potential inbreeding in the Luning chicken and Tibetan chicken population. By combining genetic differentiation index (Fst) and nucleotide diversity (θπ) ratios, we pinpointed selected regions associated with melanin deposition. Gene annotation identified 540 genes with the highest Fst value in LOC101750371 and LOC121108313, located on the 68.24–68.58 Mb interval of chromosome Z. Combining genomic and transcriptomic data, we identified ATP5E, EDN3, and LOC101750371 as candidate genes influencing skin color traits in black-bone chickens.ConclusionsThis study characterized the evolutionary history of Luning chickens and preliminarily excavated candidate genes influencing the genetic mechanism of pigmentation in black-bone chickens, providing valuable insights for the study of animal melanin deposition.

Triple-color FISH chromosome constitution and genome size analyses confirmed the ploidy of newly developed ten Hibiscus sp. cultivars with different breeding history

Triple-color FISH chromosome constitution and genome size analyses confirmed the ploidy of newly developed ten Hibiscus sp. cultivars with different breeding history

IDENTIFICATION CANDIDATE SSR, SNPs AND GENES ASSOCIATED SALT TOLERANCE IN ASIATIC COTTON (GOSSYPIUM ARBOREUM)

Soil is a vital resource for feeding the growing global population. Increased salt tolerance of perennial species used for fodder or fuel production is an important and natural method for controlling the spread of secondary salinity. This study was carried out to identify marker-trait association analysis using 7 traits and one comprehensive index of salt tolerance (CIST) and SSR and SNP markers for 215 accessions of Asiatic cotton (G. arboretum). The traits related to salt tolerance like germination rate (GR), fresh weight (FW), stem length (SL), water content (WC), chlorophyll content (ChlC), electric conduct (EC) and methylene dioxyamphetamine (MDA), of 215 cotton accessions were screened out using 150mM NaCl concentration after 7 days of seed growth. According to a comprehensive index of salt tolerance (CIST), 215 accessions were mainly categorized into four groups, and 11 accessions (top 5%) with high salinity tolerance were selected for breeding. Group 1 contained 12 accessions that were sensitive to high salt treatment (<0.6), group 2 contained 26 accessions that were moderate tolerant to salt treatment (0.6～1.5), group 3 includes 153 accession that were tolerant (1.5～2.5), and group 4 had 24 accessions that were highly tolerant to salt treatment (>2.5). The natural population of 215 accessions of G. arboretum was first classified into 3 main groups by phylogenic analysis, in which Group 2 (G2) and Group 3 (G3) represented the Yellow River and Yangtze River accessions respectively, while Group 1 (G1) contained mixed cotton accessions which belongs to different cotton growing areas in China. The grouped accessions results were largely congruent with the breeding history and ecological region, which indicates the extensive genetic diversity of G. arboretum accessions both in phenotype and genotype. The relative value (R) of the traits was used for marker-trait association analysis. Twenty-two strong SSR marker-trait associations were obtained with strict significant P value i.e. P< 0.01 and four makers including NAU1023, NAU1099, JESPR222, and NAU2783 were significantly related to salt tolerance. The marker NAU2783 was highest associated (P= 1.98E-12) with REC, and with the highest phenotype variation of 20.87%. Some markers are significantly associated with more than two traits. MUSS020 was significantly (P<0.01) related with RFW, and RMDA, NAU1375 was associated with RFW and RSL, while NAU3468 was significantly associated with RFW, RGR, and RWC. By applying the threshold of –log10 P≥4.0, the 2062 SNP markers covered all 13 chromosomes and 100 SNP markers locations that were unknown. Among these 2062 marker‐trait associations, 61 markers were associated with RGR, 187 markers were associated with RFW, 255 markers were associated with RSL, 370 markers were associated with RWC, 190 markers were associated with RChlC, 583 markers were associated with REC, 335 markers were associated with RMDA and 81 markers were associated with CIST. The nine SNP rich regions analysis revealed 143 polymorphisms that distributed 40 candidate genes and significantly associated with salt tolerance. Notably, two SNP rich regions on chromosome 7 were found to be significantly associated with two salinity related traits, RFW and RSL, by the threshold of −log10P ≥ 6.0, and two candidate genes (Cotton_A_37775 and Cotton_A_35901) related to two key SNPs (Ca7_33607751 and Ca7_77004962) were possibly associated with salt tolerance in G. arboreum. The classification information derived from these studies may be used to facilitate the development of salt tolerant cotton accessions that could give economic yield in salinity prone areas. The strong marker-trait association results might provide insights for marker-assistant selecting salt-tolerant varieties and will be useful for future cotton breeding programs.