Guangxi indigenous chickens represent valuable genetic resources characterized by diverse phenotypic features, disease resistance, and superior meat quality, making them ideal breeding materials for modern breeding systems. Elucidating the genetic basis underlying these traits in Guangxi indigenous chickens is crucial for further advancements in breeding programs. In the current study, using whole-genome sequencing, we performed comprehensive genomic analyses to characterize the genetic diversity, population structure, demographic history and selection signatures for seven Guangxi indigenous chicken breeds and two commercial breeds. The results of genetic diversity indices and effective population size demonstrated Guangxi indigenous chicken breeds maintain significantly higher genetic diversity and have undergone less intensive artificial selection than commercial breeds. Population genetic analyses revealed obvious geographic stratification, dividing Guangxi chicken breeds into southern and northern clusters. Southern populations showed closer genetic affinity to red junglefowl (Gallus gallus spadiceus) than northern populations, suggesting differential selection patterns. Genome-wide selection scans identified strong signals between southern and northern populations, uncovering genes associated with pigmentation (BCO2, SOX10, GRM5, MC1R, MITF, EDN3), body size (IGF1, POU1F1, CDH12) and egg production (AKT3, WDR25). Additionally, comparative genomic analysis with commercial breeds identified divergent selection at loci governing genes related to growth, reproduction, disease resistance and environmental adaptability, such as IGF1, LRP1B, GLI3, CDH7, KIF18A, ROBO2, EVA1A, IKZF1, GRID2, and EPHA7. These selection patterns likely reflect the unique genomic features of Guangxi indigenous chickens, shaped by ecological adaptations, traditional husbandry practices, and consumer preferences. Our findings offer new perspectives on the genetic architecture of Guangxi indigenous chickens, facilitating their conservation and utilization in modern breeding programs.

Abstract High-intensity selection has dramatically increased growth rate and daily weight gain in broilers, but the accompanying problem is the excessive deposition of abdominal fat. According to our previous transcriptome analysis, insulin-like growth factor binding protein 2 (IGFBP2) and miR-1434 were identified as involved in abdominal fat. In this study, we further investigated their function in the proliferation and differentiation of chicken preadipocytes. The results indicated that overexpression of IGFBP2 promoted the proliferation and differentiation of preadipocytes, while interference of IGFBP2 inhibited cell proliferation and lipogenic differentiation. The regulatory effect of miR-1434 on the proliferation and differentiation of preadipocytes was opposite to that of IGFBP2. Dual-luciferase reporter assay proved that miR-1434 directly binds to the 3'-untranslated region (3'UTR) of IGFBP2. As expected, the miR-1434 mimics eliminated the impact of the overexpression vector of IGFBP2 on preadipocytes. In brief, we revealed that miR-1434 promoted the proliferation and differentiation of preadipocytes by blocking IGFBP2expression, thus impacting deposition in broilers. These findings may provide a novel target for improving chicken meat quality.

Fat deposition is a vital factor affecting the economics of poultry production. Numerous studies on fat deposition have been done. However, the molecular regulatory mechanism is still unclear. In the present study, the whole-transcriptome RNA sequencing in abdominal fat, back skin, and liver both high- and low-abdominal fat groups was used to uncover the competitive endogenous RNA (ceRNA) regulation network related to chicken fat deposition. The results showed that differentially expressed (DE) genes in abdominal fat, back skin, liver were 1207(784 mRNAs, 330 lncRNAs, 41 circRNAs, 52 miRNAs), 860 (607 mRNAs, 166 lncRNAs, 26 circRNAs, 61 miRNAs), and 923 (501 mRNAs, 262 lncRNAs, 15 circRNAs, 145 miRNAs), respectively. The ceRNA regulatory network analysis indicated that the fatty acid metabolic process, monocarboxylic acid metabolic process, carboxylic acid metabolic process, glycerolipid metabolism, fatty acid metabolism, and peroxisome proliferator-activated receptor (PPAR) signaling pathway took part in chicken fat deposition. Meanwhile, we scan the important genes, FADS2, HSD17B12, ELOVL5, AKR1E2, DGKQ, GPAM, PLIN2, which were regulated by gga-miR-460b-5p, gga-miR-199-5p, gga-miR-7470-3p, gga-miR-6595-5p, gga-miR-101-2-5p. While these miRNAs were competitive combined by lncRNAs including MSTRG.18043, MSTRG.7738, MSTRG.21310, MSTRG.19577, and circRNAs including novel_circ_PTPN2, novel_circ_CTNNA1, novel_circ_PTPRD. This finding provides new insights into the regulatory mechanism of mRNA, miRNA, lncRNA, and circRNA in chicken fat deposition.

为了解广西地方鸡的肉质特征,且为进一步推动广西地方鸡品种选种选育提供基础依据,对广西南丹瑶鸡(NDY)、霞烟鸡(XY)、广西三黄鸡(SH)、龙胜凤鸡(LSF)、广西麻鸡(GXM)和东兰乌鸡(DLW)6个地方鸡品种以及艾维茵快大型商品肉鸡于上市日龄进行屠宰,采集胸肌和腿肌,利用仪器分别测定了肉色、电导率、pH、剪切力、肌内脂肪含量等共14个指标.结果显示:广西麻鸡公鸡的胸肌和腿肌Opto值(比色值)显著高于其他品种(P<0.05);东兰乌鸡腿肌肌内脂肪含量显著高于其他地方鸡品种(P<0.05),霞烟鸡胸肌肌内脂肪含量最高但仅与南丹瑶鸡、东兰乌鸡和艾维茵鸡差异显著(P<0.05);龙胜凤鸡胸肌的肌肉电导率45 min最高且除与霞烟鸡和艾维茵鸡差异不显著外(P>0.05),与其他四个地方鸡都差异显著(P<0.05),但腿肌电导率45 min最高为霞烟鸡且除与艾维茵鸡差异不显著外(P>0.05),与其他五个地方鸡品种都差异显著(P<0.05);龙胜凤鸡母鸡胸肌的肌内脂肪含量和剪切力均显著高于其他品种(P<0.05),腿肌的肌内脂肪含量也最高但仅与广西三黄鸡、广西麻鸡和南丹瑶鸡差异显著(P<0.05),腿肌剪切力最高的为广西麻鸡,且除与龙胜凤鸡差异不显著(P>0.05)外和其他品种鸡都差异显著(P<0.05);霞烟鸡胸肌和腿肌的电导率45 min都显著高于其他品种(P<0.05).由此可知,广西麻鸡和广西三黄鸡胸肌腿肌的色泽鲜亮,霞烟鸡公鸡胸肌部位风味相对较好,而腿肌部位则是东兰乌鸡风味较好,龙胜凤鸡公鸡和霞烟鸡母鸡的肌肉电导率较高,一定程度上反映出肌肉系水能力弱.

为深入了解广西地方鸡种肌肉的营养价值,本实验选取120日龄广西三黄鸡、南丹瑶鸡、广西麻鸡、广西乌鸡(东兰乌鸡)和霞烟鸡5个广西地方鸡种各20只,公、母各半,测定其胸肌和腿肌肌肉氨基酸的组成和含量.基于联合国粮农组织和世界卫生组织(FAO/WHO)标准模式谱对其营养价值进行评定.结果显示:在5个广西地方鸡种中,霞烟鸡的必需氨基酸含量、氨基酸总量和味觉氨基酸含量最高,分别为16.88、42.76、22.95 g/100g;5个地方鸡种胸肌和腿肌的必需氨基酸含量存在一定差异,且胸肌显著高于腿肌;不同品种胸肌和腿肌的必需氨基酸/氨基酸总量(EAA/TAA)、必需氨基酸/非必需氨基酸(EAA/NEAA)均符合FAO/WHO提出的理想蛋白源标准;缬氨酸是广西三黄鸡的第一限制性氨基酸,蛋氨酸+胱氨酸是其他4个品种的第一限制性氨基酸.5个地方鸡种的胸肌和腿肌具有丰富的味觉氨基酸,风味氨基酸/氨基酸总量均高于50％,且腿肌比胸肌风味更佳.

Comb traits have potential economic value in the breeding of indigenous chickens in China. Identifying and understanding relevant molecular markers for comb traits can be beneficial for genetic improvement. The purpose of this study was to utilize genome-wide association studies (GWAS) to detect promising loci and candidate genes related to comb traits, namely, comb thickness (CT), comb weight (CW), comb height, comb length (CL), and comb area. Genome-wide single-nucleotide polymorphisms (SNPs) and small insertions/deletions (INDELs) in 300 Nandan-Yao chickens were detected using whole-genome sequencing. In total, we identified 134 SNPs and 25 INDELs that were strongly associated with the five comb traits. A remarkable region spanning from 29.6 to 31.4 Mb on chromosome 6 was found to be significantly associated with comb traits in both SNP- and INDEL-based GWAS. In this region, two lead SNPs (6:30,354,876 for CW and CT and 6:30,264,318 for CL) and one lead INDEL (a deletion from 30,376,404 to 30,376,405 bp for CL and CT) were identified. Additionally, two genes were identified as potential candidates for comb development. The nearby gene fibroblast growth factor receptor 2 (FGFR2)-associated with epithelial cell migration and proliferation-and the gene cytochrome b5 reductase 2 (CYB5R2)-identified on chromosome 5 from INDEL-based GWAS-are significantly correlated with collagen maturation. The findings of this study could provide promising genes and biomarkers to accelerate genetic improvement of comb development based on molecular marker-assisted breeding in Nandan-Yao chickens.

BACKGROUND:Egg production is a very important economic trait in chicken breeding, but its molecular mechanism is unclear until now. Nandan-Yao chicken (Gallus gallus domesticus) is a native breed in Guangxi province, China, which is famous for good meet quality, but with low egg production. METHODS:To explore the molecular regulation related to egg production, high egg production (HEP) and low egg production (LEP) were divided according to the total egg number at 55 weeks, and the concentration of serum sex hormones was tested to evaluate the physiological function of ovary and uterus. RNA sequencing (RNA-Seq) was used to explore the transcriptome from the ovary and uterus of Nandan-Yao chicken. RESULTS:The levels of serum sex hormone showed that concentrations of estradiol (E2), follicle-stimulating hormone (FSH), and luteotropic hormone (LH) were significantly higher in HEP than those in LEP (P < 0.01), while the concentration of testosterone (T) was significantly lower in HEP (P < 0.01). RNA-Seq analysis identified 901 and 2763 differentially expressed genes (DEGs) in ovary and uterus, respectively. Enrichment analysis showed that DEGs were significantly involved in the regulation of tight junction in the ovary (P < 0.05), while in uterus, DEGs were mainly enriched in the phagosome, ECM-receptor interaction, cell adhesion molecules (CAMs), focal adhesion, cardiac muscle contraction, cytokine-cytokine receptor interaction, and the regulation of MAPK signaling pathway (P < 0.05). Protein network interaction and function analyses revealed that FN1, FGF7, SOX2 identified from the ovary, and UQCRH, COX5A, FN1 from the uterus might be key candidate genes for egg production in Nandan-Yao chicken. CONCLUSIONS:Our study provided key candidate genes and pathways involved in the egg-laying process of Nandan-Yao chicken and could help to further understand the molecular mechanisms of chicken reproduction.

蛋重和蛋形指数是地方鸡育种过程中蛋品质测定的两个重要性状,会一定程度影响孵化成绩.为探究广西6个地方鸡品种蛋重和蛋形指数的变化规律及其与孵化成绩的关系,将广西三黄鸡(SH)、霞烟鸡(XY)、广西麻鸡(GXM)、南丹瑶鸡(NDY)、龙胜凤鸡(LSF)、东兰乌鸡(DLW)6个地方鸡品种与作为对照的来航鸡(LH)比较,在相同的饲养条件下,对其整个产蛋期的蛋重和蛋形指数及对应孵化成绩进行分析研究.结果 显示,广西地方鸡品种的蛋重随着产蛋周龄的增加而增加,产蛋后期显著高于产蛋前期(P＜0.05),蛋形指数随着产蛋周龄的增加呈上升趋势.来航鸡的蛋重显著高于广西地方鸡(P＜0.05).应用判别分析可对本研究6个地方品种受精蛋的孵化情况进行预测和预选.该研究为广西地方品种蛋重和蛋形指数的选种选育提供理论依据.

为了探讨蛋壳颜色形成的分子基础,从分子水平提高南丹瑶鸡的选种选育,以整个产蛋周期(24～60周龄)256只南丹瑶鸡蛋壳颜色为研究对象,利用多重PCR测序的方法检测蛋壳颜色相关基因,用单因素方差分析检测得到的SNP与蛋壳颜色的相关性.结果 显示:在检测的92个位点中,与32周龄、40周龄、48周龄、56周龄蛋壳颜色显著相关的位点各1个(P＜0.05),与36周龄、52周龄蛋壳颜色显著相关的位点各4个(P＜0.05),与44周龄蛋壳颜色显著相关的位点2个(P＜0.05),与60周龄蛋壳颜色显著相关的位点7个(P＜0.05);其中Chr4_16561950、Chr1 85290873两个SNP位点可作为蛋壳颜色性状选育位点.研究结果为南丹瑶鸡蛋壳颜色形成的分子机理提供了理论依据,为提高其蛋壳颜色的均匀度提供了分子标记.

为了探讨适合选作“冰鲜鸡”的广西地方鸡品种,试验以南丹瑶鸡、广西麻鸡、广西三黄鸡和霞烟鸡为研究对象,测定了其屠体重、法氏囊重、胸肌重、毛孔数,计算胸肌和法氏囊在屠体中的占比,比较这些性状指标在4个品种之间的差异,并分析了屠体重和法氏囊重之间的相关性.结果 表明:在公鸡中,南丹瑶鸡和霞烟鸡屠体重差异不显著(P＞0.05),且均极显著低于广西麻鸡和广西三黄鸡(P＜0.01);广西麻鸡屠体重、法氏囊重极显著高于其他3个品种(P＜0.01);广西三黄鸡法氏囊在屠体中的占比和胸肌重仅次于广西麻鸡.在母鸡中,广西麻鸡屠体重极显著高于南丹瑶鸡、广西三黄鸡和霞烟鸡(P＜0.01),毛孔数极显著低于霞烟鸡、南丹瑶鸡、广西三黄鸡(P＜0.01);南丹瑶鸡的法氏囊重极显著高于广西麻鸡、广西三黄鸡和霞烟鸡(P＜0.01);广西麻鸡的法氏囊在屠体中的占比最低,极显著低于南丹瑶鸡和广西三黄鸡(P＜0.01).南丹瑶鸡公、母鸡屠体重与法氏囊呈极显著相关(P＜0.01),相关系数分别为0.759和0.503;广西三黄鸡屠体重和法氏囊重在公鸡中呈极显著相关(P＜0.01,相关系数为0.487),在母鸡中呈显著相关(P＜0.05,相关系数为0.431);广西麻鸡和霞烟鸡屠体重与法氏囊重相关性不显著(P＞0.05).说明与广西三黄鸡、霞烟鸡和南丹瑶鸡相比,广西麻鸡具有更好的屠体外观,是适于培育屠宰“冰鲜鸡”的良好素材.

本文以广西富凤农牧集团有限公司饲养的895只28周龄的广西麻鸡母鸡连续26天产蛋数据为依据,对广西麻鸡个体产蛋规律进行了初步分析和研究.结果表明,在统计期内,平均个体产蛋量为15.77±0.25个,最高个体产蛋量为28个,母鸡产蛋量大多数集中在16个～25个,这些母鸡的产蛋数占总产蛋数的90％.大部分母鸡在上午产蛋,上午产蛋数占产蛋总数的59％,且个体产蛋总数与上午产蛋数呈极显著正相关(p<0.01).经相关性分析,母鸡个体产蛋数与连产天数呈极显著正相关(p<0.01),与产蛋间隔呈极显著负相关(p<0.01).广西麻鸡就巢性较强,研究发现,母鸡个体产蛋数与抱窝天数呈极显著负相关(p<0.01).研究可为广西麻鸡进一步的育种工作提供数据支撑.

为了研究广西地方鸡品种东兰乌鸡不同周龄蛋品质及其变化规律,试验在饲养条件相同的条件下,测定了东兰乌鸡不同周龄(28,32,36,40,44,48,52,56,60周龄)的蛋品质指标,检测指标包括蛋重、蛋形指数、蛋黄颜色、哈氏单位、蛋壳比率、蛋壳强度、蛋壳厚度、蛋黄比率.结果 表明:蛋重随着产蛋周龄的增加而增大,产蛋后期显著高于产蛋前、中期(P＜0.05),蛋形指数和蛋黄比率随着产蛋周龄的增加呈上升趋势,蛋壳强度和蛋壳比率随着产蛋周龄的增加呈下降趋势,蛋壳厚度、哈氏单位和蛋黄颜色在整个产蛋周期内无明显的变化规律.总体而言,东兰乌鸡蛋蛋重较小、蛋壳较薄、蛋形规则、蛋白浓稠、蛋黄比率高、蛋黄颜色适中.说明东兰乌鸡作为广西地方鸡品种具有较好的蛋品质,且在不同产蛋期的蛋品质具有一定的变化规律.

为了探讨南丹瑶鸡优良蛋品质的分子基础,试验以256只产蛋期南丹瑶鸡为研究对象,测定其在整个产蛋周期(24～60周)所产蛋的蛋品质,同时翅静脉采血提取基因组DNA,利用多重PCR技术检测与蛋品质相关基因的SNP位点,并对SNP位点与蛋白高度、蛋黄颜色、蛋壳厚度、蛋壳强度、蛋形指数、蛋重及哈氏单位等7个蛋品质性状进行关联分析.结果表明:南丹瑶鸡蛋品质变异大.蛋白高度分别在32,40,48,52,56周龄关联到的显著SNP位点有1,2,1,1,1个;蛋黄颜色分别在28,56,60周龄关联到的显著SNP位点有1,2,1;蛋壳厚度分别在40,60周龄关联到的显著SNP位点有6,2个;蛋壳强度分别在36,48,56周龄关联到的显著SNP位点有2,1,1个;蛋形指数分别在24,32,40周龄关联到的显著SNP位点有1,1,1个;蛋重分别在32,48,56周龄关联到的显著SNP位点有2,1,2个;哈氏单位分别在36,40,48,56周龄关联到的显著SNP位点有1,1,1,1个.南丹瑶鸡具有优秀的蛋品质,筛选得到的与不同周龄南丹瑶鸡蛋品质显著相关的SNP位点有chr1_65234293、chr1_65234317、chr1_65234336、chr1_65258207、chr1_68526266、chr1_68526267、chr1_68526344、chr1 _68526357、chr1 _85290991、chr12_3349578、chr12_3351761、chr4_16561900、chr4_16561922、chr4_16562030、chr4_16562070、chr9_4769768、chr9_4771619、chr9_4771623、chr9_4771738、chr9_4771779、chr9_4772495共21个.说明试验筛选出的SNP位点可用于南丹瑶鸡的育种.

为了研究广西地方鸡品种120日龄体尺性状,以及探究各体尺性状之间的相关性.对广西地方鸡品种南丹瑶鸡、霞烟鸡、广西三黄鸡、龙胜凤鸡、广西麻鸡、东兰乌鸡在120日龄的体重、体尺共8个性状进行测定分析.结果:除了南丹瑶鸡母鸡髋宽显著大于公鸡外(p<0.05),其它体重体尺性状公鸡均显著大于母鸡(p<0.05).霞烟鸡体重、体尺指标变异系数在6个地方鸡品种中最小(<10％).6个品种公母鸡的体重在体重体尺指标中变异系数均最大,此外龙胜凤鸡母鸡髋宽变异系数(10.47％)明显大于其他品种.比较6个品种公母鸡体重体尺性状,发现在部分品种中同一体尺性状间无显著性差异(p>0.05).结果表明,6个品种地方鸡胫长和胫围与其他体尺性状之间的相关性较低,在有些品种中相关性不显著(p>0.05),除胫长、胫围外其他体重体尺性状间均存在极显著相关(p<0.01).