Identification of genomic characteristics and selective signals in Guizhou black goat

BACKGROUND

Guizhou black goat is one of the indigenous black goat breeds in the southwest region of Guizhou, China, which is an ordinary goat for mutton production. They are characterized by moderate body size, black coat, favorite meat quality with tender meat and lower odor, and tolerance for cold and crude feed. However, little is known about the genetic characteristics or variations underlying their important economic traits.

RESULTS

Here, we resequenced the whole genome of Guizhou black goat from 30 unrelated individuals breeding in the five core farms. A total of 9,835,610 SNPs were detected, and 2,178,818 SNPs were identified specifically in this breed. The population structure analysis revealed that Guizhou black goat shared a common ancestry with Shaanbei white cashmere goat (0.146), Yunshang black goat (0.103), Iran indigenous goat (0.054), and Moroccan goat (0.002). However, Guizhou black goat showed relatively higher genetic diversity and a lower level of linkage disequilibrium than the other seven goat breeds by the analysis of the nucleotide diversity, linkage disequilibrium decay, and runs of homozygosity. Based on FST and θπ values, we identified 645, 813, and 804 selected regions between Guizhou black goat and Yunshang black goat, Iran indigenous goat, and cashmere goats. Combined with the results of XP-EHH, there were 286, 322, and 359 candidate genes, respectively. Functional annotation analysis revealed that these genes are potentially responsible for the immune response (e.g., CD28, CD274, IL1A, TLR2, and SLC25A31), humility-cold resistance (e.g., HBEGF, SOSTDC1, ARNT, COL4A1/2, and EP300), meat quality traits (e.g., CHUK, GAB2, PLAAT3, and EP300), growth (e.g., GAB2, DPYD, and CSF1), fertility (e.g., METTL15 and MEI1), and visual function (e.g., PANK2 and NMNAT2) in Guizhou black goat.

CONCLUSION

Our results indicated that Guizhou black goat had a high level of genomic diversity and a low level of linkage disequilibrium in the whole genome. Selection signatures were detected in the genomic regions that were mainly related to growth and development, meat quality, reproduction, disease resistance, and humidity-cold resistance in Guizhou black goat. These results would provide a basis for further resource protection and breeding improvement of this very local breed.

Functional components profile and glycemic index of kidney beans

Low glycemic index (GI) diet has been considered as a strategy for type II diabetes patients. In the present study, the phenolics profile, α-amylase inhibitor activities, starch composition as well as the glycemic index of seven varieties of kidney beans were studied. An enzymatic inhibitory reaction model was employed to determine the α-amylase inhibitor activity, and the in vitro digestion model coupled with the 3, 5-dinitrosalicylic acid colorimetry method was adopted to evaluate the starch composition and glycemic index. The results showed that gallic acid was dominant in kidney beans, and the colored beans contained more phenolics than the white ones. In addition, the α-amylase inhibitor activities of kidney beans ranged from 1.659 ± 0.050 to 4.162 ± 0.049 U/g DW, among which the Y2 variety was the top-ranked. Furthermore, kidney beans starch demonstrated brilliant resistance to digestion with the contribution of resistant starch to total starch between 70.90 ± 0.39% and 83.12 ± 0.42%. Eventually, these kidney beans were categorized as low GI foods, which ranged from 32.47 ± 0.13 to 52.99 ± 0.56, the resistant starch makes dominant contribution to the low GI. These results indicate that kidney beans can be served as ingredients in functional low GI foods.