Hybrid Selection Research Articles

Traits and underlying genetics important for low‐input organic sorghum production

AbstractSorghum [Sorghum bicolor (L.) Moench] is a potential crop for organic production that could help meet the demand increase in organic food products and feed grains, but no efforts have been made to improve sorghum breeding tools, techniques, and methods for this cropping system. Based on revelations in other crops, focal traits and their prioritization to optimize sorghum for organic use likely differs from conventional sorghum breeding targets. This study evaluated yield performance, agronomic characteristics, and biotic stress resistance under certified organic practices in a range of grain sorghum genotypes that included 70 hybrids, 72 advanced breeding lines, and 43 diverse accessions, as well as 10 sweet sorghum cultivars and four commercial maize hybrids. Multiyear, multilocation trial data demonstrated that sorghum can be effectively produced using sustainable and organic inputs, but hybrid or cultivar selection is extremely important for success as entry means for grain yield ranged from 26 to 5,970 kg ha−1. Yields of top sorghum entries rivaled commercially available maize (Zea mays) hybrids. Overall, hybrids significantly outperformed inbred lines as heterosis proved beneficial for influential agronomic traits, although a Clemson F6 advanced breeding line, PV20_0426, ranked second in yield. Sugarcane aphid tolerance, increased canopy closure, and grain mold resistance were positively correlated with grain yield and should be considered target traits for breeding sorghum hybrids and cultivars for organic use. Depending on possible seed production constraints, developing pure line cultivars with the proper trait package may be effective to diminish this potential obstacle for the organic sorghum market.

Використання комплексних підходів добору цінних генотипів рослин буряків цукрових за створення батьківських компонентів гібридів на ЦЧС основі

Goal. To study and compare the effectiveness of different directions of selection of valuable plant genotypes for the creation of parental components of sugar beet hybrids on a cytoplasmic male sterile (CMS) basis. Methods. Field — experiments, phenological observations, laboratory — to determine laboratory germination and sugar content, measuring and weighing — to determine the crop structure, statistical — to process mathematically the achieved results. Results. It is established that the use of integrated approaches to the selection of the best genotypes of plants contributes to the creation of combination-valuable parental components of sugar beet hybrids with increased base productivity. In terms of root crop yield, the average indicators of CMS of lines were 107.4%, sugar yield — 106.3, sugar output — 105.5% compared to the group standard. The sugar content of their roots was at the standard level. The yield of roots of multi-sprout pollinators increased to 116.7%, sugar yield — to 118.3, sugar output — to 116.7% to the group standard. In general, new selection materials of sugar beets of yield direction of productivity were created by complex selection. The corresponding performance indicators of CMS lines and multi-sprout pollinators created using 2 other areas of selection were at or below the standard. According to the results of testing experimental hybrids created with the participation of parent components with increased basic productivity, 8 high-yielding hybrids were identified, which in terms of root yield exceed the group standard by 19.7–27.2%, sugar yield, and output — by 17.6–25, 7% and 16.9–25.5%, respectively. Conclusions. The introduction of complex selection in the selection process of sugar beets significantly increases its efficiency, allows, from the standpoint of a systematic approach, to evaluate existing and form a new source material for the selection of parent components and hybrids on a CMS basis with high productivity potential (sugar yield 11–12 t/ha), suitable for energy and environmentally friendly cultivation technologies.

Relationship between genetic distance based on single nucleotide polymorphism markers and hybrid performance in Robusta coffee (Coffea canephora)

AbstractThe choice of parents is a vital first step in any variety development process. This is particularly imperative in tree crops that require minimally 15–20 years to complete a varietal development. The present study was conducted to determine genetic distances (GDs) between parental clones of Robusta coffee hybrids and assess the relationship between GD and hybrid performance. The experimental material consisted of 64 parental clones and 56 hybrids. The hybrids were evaluated over 11 years, planted in a randomized complete block design with six replications. GD among parental clones was determined based on 120 SNP markers. The results revealed a significant correlation (r = 0.351, p < 0.0082) between GD of parental clones and yield performance of their hybrids. Posterior selection of highest GD hybrids revealed an increase in yield gain over general mean with increasing GD between parental clones of hybrids. Furthermore, comparison of inter‐ and intra‐population hybrids classified using Bayesian clustering analysis revealed consistent outcome where inter‐group hybrids outperformed intra‐group hybrids for cumulative yield. These results supported the hypothesis that GD is related to the yield performance of Robusta coffee hybrids and is an efficient predicator of hybrid performance for yield.

Application of deterministic, stochastic, and hybrid methods for cloud provider selection

Cloud Computing popularization inspired the emergence of many new cloud service providers. The significant number of cloud providers available drives users to complex or even impractical choice of the most suitable one to satisfy his needs without automation. The Cloud Provider Selection (CPS) problem addresses that choice. Hence, this work presents a general approach for solving the CPS problem using as selection criteria performance indicators compliant with the Cloud Service Measurement Initiative Consortium - Service Measurement Index framework (CSMIC-SMI). To accomplish that, deterministic (CPS-Matching and CPS-DEA), stochastic (Evolutionary Algorithms: CPS-GA, CPS-BDE, and CPS-DDE), and hybrid (Matching-GA, Matching-BDE, and Matching-DDE) selection optimization methods are developed and employed. The evaluation uses a synthetic database created from several real cloud provider indicator values in experiments comprising scenarios with different user needs and several cloud providers indicating that the proposed approach is appropriate for solving the cloud provider selection problem, showing promising results for a large-scale application. Particularly, comparing which approach chooses the most appropriate cloud provider the better, the hybrid one presents better results, achieving the best average hit percentage, dealing with simple and multi-cloud user requests.

Object-Based Multigrained Cascade Forest Method for Wetland Classification Using Sentinel-2 and Radarsat-2 Imagery

The development of advanced and efficient methods for mapping and monitoring wetland regions is essential for wetland resources conservation, management, and sustainable development. Although remote sensing technology has been widely used for detecting wetlands information, it remains a challenge for wetlands classification due to the extremely complex spatial patterns and fuzzy boundaries. This study aims to implement a comprehensive and effective classification scheme for wetland land covers. To achieve this goal, a novel object-based multigrained cascade forest (OGCF) method with multisensor data (including Sentinel-2 and Radarsat-2 remote sensing imagery) was proposed to classify the wetlands and their adjacent land cover classes in the wetland National Natural Reserve. Moreover, a hybrid selection method (ReliefF-RF) was proposed to optimize the feature set in which the spectral and polarimetric decomposition features are contained. We obtained six spectral features from visible and shortwave infrared bands and 10 polarimetric decomposition features from the H/A/Alpha, Pauli, and Krogager decomposition methods. The experimental results showed that the OGCF method with multisource features for land cover classification in wetland regions achieved the overall accuracy and kappa coefficient of 88.20% and 0.86, respectively, which outperformed the support vector machine (SVM), extreme gradient boosting (XGBoost), random forest (RF), and deep neural network (DNN). The accuracy of the wetland classes ranged from 75.00% to 97.53%. The proposed OGCF method exhibits a good application potential for wetland land cover classification. The classification scheme in this study will make a positive contribution to wetland inventory and monitoring and be able to provide technical support for protecting and developing natural resources.

Optimization of source material creation, selection of new hybrids and their variety testing in conditions of the Bukovina region

Optimization of source material creation, selection of new hybrids and their variety testing in conditions of the Bukovina region

Maize topcrosses for yield performance by additive main effects and multiplicative interaction analysis

ABSTRACT: The analysis of main additive effects and multiplicative interaction is commonly used in the evaluation of the genotype x environment interaction, however, its application can be used for other purposes, as it is performed in the presentresearch, which uses this technique in the selection of inbred lines, testers and hybrids in maize topcrosses. Thisresearch determined the effect of the inbred lines x testers interaction through the analysis of main additive effects and multiplicative interaction, verifying their efficiency in the selection of inbred lines, testers and hybrid combinations in topcrosses. The trials were carried out in the 2015/16 and 2016/17 crop seasons, with a complete block design, with three replications. Thirty S3 maize inbred lines were evaluated in crosses with the AG8025, P30B39, MLP102, 60.H23.1 and 70.H26.1 testers forming 150 hybrids topcrosses. The trait evaluated was grain yield. The adaptability and stability of testers and inbred lines were evaluated by the methodology of analysis of main additive effects and multiplicative interaction directed to the interaction of testers x inbred lines. The 96.3 inbred line has the most homogeneous performance and the highest grain yield, considering the crossing with all testers in both environments. The 70.H26.1 tester is considered the most stable and the most recommended for topcrosses. The best specific combinations were 96.3 x 70.H26.1 and 96.3 x 60.H23.1.

Creation of new starting material for the selection of high-product quick maize hybrids, adapted to the conditions of the Western Forest-Steppe of Ukraine

Creation of new starting material for the selection of high-product quick maize hybrids, adapted to the conditions of the Western Forest-Steppe of Ukraine

PROSPECTS FOR BREEDING WINTER COMMON WHEAT FOR RESISTANCE TO LEAF RUST USING MOLECULAR MARKERS

Wheat leaf rust is a harmful disease whose epiphytotics lead to serious grain yield losses. Severe epiphytoties of leaf rust are observed once every 3-4 years in the Volga Region. Despite numerous breeding achievements, many modern wheat varieties in the Russian Federation are not resistant to leaf rust. Studies of the newest assortment of soft wheat, carried out by Russian researchers, show that the genotypes of 93% of the studied varieties contained Lr genes individually or in various combinations; the Lr34 gene is widely represented in combinations with the ineffective juvenile genes Lr3, Lr10 and Lr26, which provides an acceptable level of field resistance to leaf rust. Selection for resistance is hampered by the constant change in the race composition of the pathogen, which goes hand in hand with the introduction of highly expressed genes of vertical resistance into the wheat genotype by breeders. The priority in breeding is the use of "field" or long-term resistance. There are suggestions that this type of resistance is due to the additive effects of several genes that cause the effects of age resistance and "slow rusting”. Development of cultivars possessing "pyramids" of genes will produce a long-term effect of resistance. However, the use of classical methods of hybridological analysis and phytopathological tests for gene pyramiding is time-consuming and labor-intensive and not always effective. Marker-assisted selection makes it easy to identify the right alleles in both starting material and breeding lines, making it an indispensable tool in immunity breeding. The use of molecular markers makes it possible to quickly and successfully create varieties with multiple resistance genes if donors of resistance genes and specific molecular markers of these genes are available. The breeding program for winter soft wheat at the Samara Research Institute of Agriculture uses donors of genes Lr3, Lr9, Lr10, Lr26, Lr34, Lr39(41) and others, as well as a replaced chromosome 6Agi2 of wheatgrass intermediate, whose direct donors are spring soft wheat varieties ‘Tulaikovskaya 10’ and ‘Tulaikovskaya Zolotistaya’. As a result of hybridization and subsequent individual selection, promising breeding material of winter soft wheat was created in Samara Research Institute of Agriculture for further identification of valuable genotypes that contain genes of resistance to leaf rust and chromosome 6Agi2, using molecular markers.

Parent selection for hybridization in chili (Capsicum annuum L.) using multivariate analysis and K-means clustering

The study was conducted to elucidate the extent of genetic diversity of 28 chilli (Capsicum annuum L.) genotypes. Chilli plants of the selected genotypes were grown in the Field Laboratory of the Department of Genetics and Plant Breeding of Bangbandhu Sheikh Mujibur Rahman Agricultural University, Bangladesh with recommended agronomic practices. The experiment was laid out in a randomized complete block design with tree replications. The analysis of variance revealed considerable variability among the genotypes for the character studied. Genetic diversity in chilli genotypes were estimated based on 16 growth and yield contributing characters using Mahalanobis’s D2 statistics and K-means clustering. The genotypes were grouped into four different clusters by non-hierarchical clustering. Cluster III had the maximum number (13) of genotypes followed by cluster I, IV and II with 7, 5 and 3 genotypes, respectively. The highest inter-cluster genetic divergence (9.87) was recorded between clusters II and IV, whereas the highest intra-cluster distance was recorded in cluster II (4.37). Cluster II was observed to be the most important with maximum cluster means for most of the valuable traits including number of fruits per plant and number of fruit yield per plant. The characters fruit yield/plant, days to 100% fruiting, days to first flowering and individual fruit weight contributed maximum towards divergence. Considering diversity pattern and other horticultural performance the Gen7 and Gen20 from cluster I, Gen8 and Gen10 from cluster IV and Gen24 from cluster III may be taken into consideration as better parents for an efficient hybridization programme of chilli.

A Comprehensive Survey of Recent Hybrid Feature Selection Methods in Cancer Microarray Gene Expression Data

In the diagnosis and treatment of cancer, cancer classification is a vital issue. Gene selection is much needed to solve the high dimensionality issue in microarray data, small sample size, and noisy. The best way to classify cancer is to select those genes that hold the most informative ones, and this process contributes significantly to the classification performance of microarrays. In this survey, we comprehensively studied hybrid selection methods proposed since 2017 that may be used for comparison to several other algorithms proposed for gene selection in cancer classification in the past and looked to see if there are any challenges future authors that need to be discussed.

Robust Backbone Network Based on Hybrid Selection of Relays for Multi-Hop Data Dissemination in Vanets

Robust Backbone Network Based on Hybrid Selection of Relays for Multi-Hop Data Dissemination in Vanets

Evaluation of late maturity maize (Zea mays) hybrids under varying plant density and nutrient levels

Productivity of maize is influenced by selection of hybrids or improved varieties, plant population, nutrient management practices etc. These technological interventions may vary across locations. Therefore, two-year investigation was conducted during Rabi, 2019-21 at Department of Millets, Tamil Nadu Agricultural University, Coimbatore, India to evaluate the performance of late maturity maize hybrids under varying plant density and nutrient levels. The experiments were laid out in a split-split plot design replicated thrice. In the main plot, two plant densities viz., 60×25 cm and 60×20 cm spacing and in the sub plot, three nutrient levels viz., 100% RDF (250:75:75 NPK kg/ha), 90% RDF (225:68:68 NPK kg/ha) and STCR-IPNS (131:38:38 NPK kg/ha) and in the sub-sub plot, four late maturity maize hybrids viz., CMH12-686, CMH15-005, COH (M) 6 and NK6240 were tried. Based on the results of two years of experimentation, it is concluded that among the late maturity maize hybrids, CMH15-005 and CMH12-686 were found to be the most promising hybrids under a spacing of 60×20 cm with application of 100% recommended dose of fertilizer @250:75:75 NPK kg/ha. In future, these late maturity hybrids should be grown with the recommended spacing and nutrient level to achieve desirable productivity in maize.

Performance evaluation of double type tuberose IIHR-4 (IC -0633777) for flower yield. quality and biotic stress resistance/tolerance

An experiment was carried out to evaluate an advance breeding line of tuberose double type IIHR-4 along with check for flowering, yield and resistance to root knot nematode and Alternaria leaf burn disease. The hybrid selection IIHR-4 was developed through hybridization by crossing Mexican Single x Pearl Double, followed by selection. Double type tuberose IIHR-4 was found to be novel with better flowering and quality traits such as short spike (62.00 cm), rachis length (25.59cm), diameter of floret (4.47cm) and number of florets per spike (50.75). The spikes of IIHR-4 exhibited more number of florets open at a time in spike (7.10) with the shorter internodal length of 3.45cm. The florets are with shorter length (5.22cm) arranged very compactly on the spike making IIHR-4 ideal as cut flower. IIHR-4 was found to be highly resistant to root knot nematode Meloidogyne incognita under field conditions and tolerant to Alternaria leaf burn disease.

Simultaneous Selection of Sweet-Waxy Corn Ideotypes Appealing to Hybrid Seed Producers, Growers, and Consumers in Thailand

Multi-trait selection helps breeders identify genotypes that appeal to divergent groups of preferences. In this study, we performed simultaneous selection of sweet-waxy corn hybrids on several traits covering the perspectives of consumers (taller kernel depth, better eating quality), growers (early maturity, shorter plant stature, and high ear yield), and seed producers (high flowering synchrony, acceptable seed yield, and good plant architecture). Three supersweet corn lines and 8 waxy corn lines were intercrossed to generate 48 F1 hybrids according to North Carolina Design II, and these genotypes were laid out in a randomized complete block design with 3 replications across 2 seasons between 2017 and 2018. A sensory blind test on sweetness, stickiness, tenderness, and overall liking was conducted to assess the eating quality of steamed corn samples. Two methods of simultaneous selection, namely unweighted selection index and overall rank-sum index (ORSI), were applied to rank crosses, following all targeted groups of preferences. Genetic parameters and genetic gain were estimated to evaluate the effectiveness of those selection methods. Both approaches had similar patterns of preferable realized gain on each given trait and could identify similar top five crosses with only slight order changes, implying that these methods were effective to rank genotypes according to given selection criteria. One of the tested crosses, 101L/TSC-10 × KV/mon, consistently had the highest unweighted selection index in the dry (7.84) and the rainy (7.15) seasons and the lowest ORSI (310), becoming a promising candidate as synergistic sweet-waxy corn hybrid appealing to consumers, growers, and seed producers. The expected ideotypes of sweet-waxy corn hybrid are discussed.

Fault diagnosis for train plug door using weighted fractional wavelet packet decomposition energy entropy

As the passage for passengers to get on and off, train plug doors directly affect the operation efficiency of the train and the personal safety of passengers. This paper proposes a non-contact fault diagnosis method for train plug doors based on sound signals. First, empirical mode decomposition (EMD) is utilized to process the raw sound signals. A signal reconstruction method by selecting intrinsic mode functions (IMFs) using hybrid selection criteria is then proposed. Second, novel feature named weighted fractional wavelet packet decomposition energy entropy (WFWPDE) is developed by introducing the idea of fractional calculus and weight to wavelet packet decomposition energy entropy (WDPE). Third, a synchronous optimization strategy is proposed to optimize the weights and hyperparameters of support vector machine (SVM) synchronously. Finally, the superiority and feasibility of the proposed method are verified on field-collected data. By comparing with different fault diagnosis methods, the proposed method performs best on fault diagnosis of train plug doors, with accuracy of 97.87%.

ECONOMIC AND ECOLOGICAL PERSPECTIVES OF ENERGY WILLOW CULTIVATION BY THE YALTUSHKIVSKA EXPERIMENTAL BREEDING STATION OF THE INSTITUTE OF BIOENERGY CROPS AND SUGAR BEETS OF THE NATIONAL ACADEMY OF AGRARIAN SCIENCES OF UKRAINE

The article analyzes the peculiarities of energy consumption in Ukraine, and it is established that among the main consumers of fuel and energy resources, the largest share belongs to the agricultural sector, which is also characterized by the significant potential of biomass suitable for biofuel production. It was determined that the most promising source of thermal energy should be solid biofuel, the production of which in Ukraine is accompanied by a shortage of quality raw materials. Analysis of the problem allowed generating its solution in the form of cultivation of energy plantations of plants of short rotation, in particular energy fast-growing willow on the lands, withdrawn from the agricultural rotation. It is established that in the perspective of realization of the described solution, the priority tasks for scientific institutions of agrarian profile are selection of productive varieties and hybrids of short-rotation energy plants suitable for processing into rigid biofuels and development of technologies of their cultivation and processing. Among such organizations, the object of research was selected Yaltushkovo experimental breeding station of the Institute of bioenergy crops and sugar beet NAAS of Ukraine, that is engaged in breeding and elite seed production of agricultural and bioenergy crops, including energy willow. In scientific activities of Yaltushkivska experimental breeding station were carried out and analyzed experiments on the technology of growing energy willow for the production of solid biofuel from various aspects of the production cycle, including the introduction of nutrients, alternative treatment practices, the use of cover crops, planting patterns, biomass growth features, as well as collection systems and logistics. Prospects for the practical use of energy willow based on economic calculations made for the efficiency of a 10-hectare plantation were disclosed. EcoWillow 2.0 program was chosen as the methodological basis - the most complete tool for financial analysis of willow plantations. It was determined that special attention should be paid to reforming the provision of heat energy to the rural population through the creation of energy cooperatives on the use and cultivation of energy willow on the basis of intersectoral scientific and production integration at the local level, involving as a scientific partner of the existing USEC «All-Ukrainian scientific- educational consortium» to ensure coordination of communication between science, public, government and business.

Harmfulness of cotton bollworm caterpillars on maize hybrids

Goal. Determine the damage to modern corn hybrids by the caterpillars of the cotton bollworm, develop a point scale for assessing the damage of kernels on the cob, and calculate the direct losses of grain yield.
 Methods. Field. The studies were carried in the research fields of the Cherkasy Research Station of Bioresources of the NSC «Institute of Agriculture of NAAS» 2017—2019. The cultivation of corn was carried out in accordance with the cultivation technology recommended for the Forest-Steppe zone of Ukraine, Cherkasy region. Plot size — 56 m2, in four replicates. Placement of plots — randomized. The number of damaged corncobs of cotton scoop was determined per hectare. To calculate the number of damaged kernels per corncobs, each damaged corn cobs was opened and the number of eaten and damaged kernels was counted. To calculate the direct yield losses for each corn hybrid, the total number of kernels eaten and damaged by the caterpillars of the cotton bollworm (per hectare) was calculated, which was multiplied by the mass of 100 kernels, respectively.
 Results. The degree of harmfulness of cotton bollworm caterpillars on maize hybrids of different maturity was investigated. In 2017—2019 The corncobs are most damaged in hybrids of the mid-maturing group — 58.4%, less — in early-maturing hybrids — 41.1%, and in the middle-early ones — 47.8%. For the first time, a nine-point scale was developed for assessing the defeat of caryopses on the cob by Helicoverpa armigera Hbn. caterpillars direct losses of grain yield are calculated. It was found that significant yield losses were observed in all mid-season maize hybrids (0.185—0.280 t/ha).
 Conclusions. In the Left-Bank Forest-Steppe of Ukraine, the cotton bollworm turned out to be a dangerous pest of the generative organs of corn. Therefore, the selection of resistant hybrids to attack by caterpillars of the cotton bollworm is a key element in the protection of this crop. And the nine-point scale developed by us allows us to assess the degree of damage to caryopses by the caterpillars of Helicoverpa armigera Hbn.

Morpho-molecular Characterization of Maize Inbred Lines Accelerating Parental Selection for Hybridization

Characterization of genetic diversity is the foundation step for crop improvement, which provides a basis for analyzing combining ability and heterosis of inbred genotypes during a hybridization program. An investigation was carried out at the field laboratory of the Genetics and Plant Breeding department in Bangabandhu Sheikh Mujibur Rahman Agricultural University, to elucidate the genetic architecture by evaluating 12 morphological and 4 molecular (SSR) markers within 52 diverse S1 genotypes, and to assess the relationship of molecular and morphological GD. An almost equal amount of PCV and GCV coupled with high heritability and genetic advance for the traits cob weight (gm), NKPC, and NKPR lead to the selection of promising genotypes based on these characters. Correlation coefficient and scatter plot matrix established a positive and strong relationship of KL (mm), KW (mm), and KT (mm) with 100 kernel weight (gm) suggesting the importance of kernel morphology. Mahalanobis D2 statistics revealed the highest inter-cluster distance between I and II. The percentages of molecular variance within the population and among the population were 76% and 14 %, respectively. The optimum K-value was 5. Heatmap relying on molecular GD exposed MMIL-28, MMIL-54, and MMIL-96 as the most diverse lines. SHE analysis hypothesized the increase of richness and diversity over time. Less correlation between the divergence generated from morphological traits and molecular markers suggested that the morphological variation may be determined by environmental factors and also by genetic factors. A strategy for the effective selection of predicting parental lines for a future hybridization program was developed.

Genetic diversity in a genetically improved line of the Pacific oyster Crassostrea gigas with orange shell based on microsatellites and mtDNA data

The shell color is of interest to the shellfish industry and has been regarded as a target trait for a better commercial value. Based on an inbred variant line of the Pacific oyster Crassostrea gigas with orange shell obtained previously, a genetically improved orange-shell line was formed through hybridization and subsequent mass selection. In the present study, the genetic diversity among the base population (G0) and two successive mass-selected generations of the improved orange-shell line of C. gigas (G1 and G2) were assessed by both 15 microsatellites and mitochondrial cytochrome oxidase I sequences (mtCOI) compared to four outbred populations and three progenitor selected strains. The microsatellite results showed that the genetic variation over two generations of mass selection were maintained since no significant reduction in average number of alleles (Nα: 4.87–5.40), expected heterozygosity (He: 0.59–0.61) and expected heterozygosity (Ho: 0.48–0.54) compared with those of G0. The number of different alleles in the generations of improved orange-shell line ranged from 73 to 81 alleles, which was approximate 55–64% less than the 176–204 alleles found in the oysters from wild populations. The Nα in G0-G2 were obviously higher than that of the inbred orange-shell line without improvement. The differences in alleles in the improved orange-shell line compared to four wild populations is likely due to small broodstock size resulting in genetic drift over successive generations. Effective population size of G1 and G2 calculated by linkage disequilibrium methods was 63.2 and 89.8, respectively. On a population level, pairwise FST value (FST: 0.14–0.21) along with AMOVA analysis indicated medium to high genetic differentiation between the improved orange-shell line and outbred populations and progenitor selected strains. Overall, the results of microsatellite suggested that the genetic diversity of the improved orange shell line was not affected greatly by mass selection during the process of improvement. This study provides insight into utilization of shell color variants and future genetic improvement through selective breeding in aquaculture.